PWWPAtlas
STRUCTURAL BIOLOGY & CHEMICAL EVIDENCEDataset v1.2 · Phase 6D · Comparative experimental recognition environments

Evolution → structure → chemical evidence

Structural & Binding Landscape

Compare two native domains with their actual structural correspondence and independently measured chemical evidence.

Family chemical landscape

Compare experimental molecular environments →

Domain A · native protein context

PSIP1 PWWP1

UP:O75475:PWWP1 · Homo sapiens

Original annotation core: 1–64. Full protein architectures and analysis boundaries retain their separate source definitions.

13entries with observed core coordinates
1studied small-molecule profiles
2preparations with domain evidence
2domain-specific observations
0deposited research-ligand profiles
1studied without research structures

4 other deposited component profiles are classified separately and do not inflate studied-compound totals.

Compounds for Domain AEvolution & residuesFull experimental structure QA

1 preparation identities remain unresolved.

Domain B · native protein context

NSD3 PWWP1

UP:Q9BZ95:PWWP1 · Homo sapiens

Original annotation core: 270–333. Full protein architectures and analysis boundaries retain their separate source definitions.

11entries with observed core coordinates
11studied small-molecule profiles
11preparations with domain evidence
13domain-specific observations
9deposited research-ligand profiles
10studied without research structures

1 other deposited component profiles are classified separately and do not inflate studied-compound totals.

Compounds for Domain BEvolution & residuesFull experimental structure QA

6 preparation identities remain unresolved.

Recorded comparison · frozen coordinates

Structural correspondence

56aligned Cα residue pairs
2.530714 Årecorded least-squares RMSD
0.65374TM score normalized by stored A
0.65374TM score normalized by stored B
Open aligned molecular models & residue correspondences →

The comparison page exposes the exact least-squares transformation and canonical residue map. Core similarity does not establish the same pocket, affinity or histone preference.

Actual cross-target observations

Shared chemical identities or preparations

No shared chemical profile is identified across these domains in the curated snapshot.

PSIP1 PWWP1 · source-specific experiments

Reported observations for Domain A

Export CSV
PreparationTested target & constructMethod / endpointOriginal observationConditions & uncertaintySource & verification
BPPPREP:BPP PSIP1 PWWP
Construct not curatedHomo sapiens		 KdITC Kddirect binding affinity = 27 ± 2 µM27 µM · exact unit conversion
Experimental context
Replicates
Not curated
Uncertainty definition
fitting_error
Temperature
—
Buffer
Not curated
Conditions
{}
Qualification
Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.
 PMID:39031937 · 2024primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved
Original observation record
{
  "DMSO_percent": null,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": null,
  "assay_construct_start": null,
  "assay_record_id": "PWWP:ASSAY:0012",
  "assay_type": "ITC Kd",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": "retain_with_explicit_endpoint_and_identity",
  "baseline_assay_record": 1,
  "baseline_original": "{\"assay_record_id\": \"PWWP:ASSAY:0012\", \"assay_type\": \"ITC Kd\", \"ccd_id\": \"A1D73\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"BPP\", \"conditions\": {}, \"domain\": \"PWWP\", \"evidence_location\": \"Results; Figure 4B\", \"evidence_url\": \"https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981\", \"gene\": \"PSIP1\", \"interpretation\": \"Binding is established in solution; no PSIP1\u2013BPP crystal structure is assigned here.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": null, \"reference_id\": \"PMID:39031937\", \"role\": \"experimentally_studied_fragment_ligand\", \"uncertainty\": 2, \"units\": \"\u00b5M\", \"value\": 27, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}",
  "buffer": null,
  "ccd_id": "A1D73",
  "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json",
  "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "chemical_identity_status": "exact_single_CCD_identity",
  "component_context": null,
  "compound_name": "BPP",
  "conditions": "{}",
  "crystallographic_component_ids": null,
  "domain": "PWWP",
  "domain_id": "UP:O75475:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Results; Figure 4B",
  "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981",
  "gene": "PSIP1",
  "interpretation": "Binding is established in solution; no PSIP1\u2013BPP crystal structure is assigned here.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_report",
  "numeric_value_inferred_from_structure": 0,
  "pH": null,
  "pdb_id": null,
  "preparation_id": "PREP:BPP",
  "protein_id": "UP:O75475",
  "qualitative_result": null,
  "reference_id": "PMID:39031937",
  "remaining_uncertainty": "Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.",
  "replicates": null,
  "role": "experimentally_studied_fragment_ligand",
  "source_component_url": null,
  "source_id": "S04",
  "source_reported_uncertainty": "2",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "27",
  "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved",
  "temperature_C": null,
  "uncertainty": 2.0,
  "uncertainty_type": "fitting_error",
  "uncertainty_uM": 2.0,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 27.0,
  "value_operator": "=",
  "value_uM": 27.0,
  "verification_level": "primary_full_text_sections_verified"
}
NbH10PREP:NbH10 PSIP1 PWWP1
1–90Homo sapiens		 KdSPR apparent Kddirect binding affinity = 94.4 ± 9.1 nM0.0944 µM · exact unit conversion
Experimental context
Replicates
3
Uncertainty definition
SD
Temperature
25 °C
Buffer
50 mM Tris-HCl, 150 mM NaCl, 0.05% Tween 20
Conditions
{"protein_construct": "PSIP1 1–90", "replicates": 3, "uncertainty_type": "SD"}
Qualification
Apparent SPR affinity of a nanobody; not a small molecule or a solved nanobody–PWWP complex.
 PMID:42194065 · 2026local_primary_full_text_XML_table_and_methods_verified
Original observation record
{
  "DMSO_percent": null,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": 90,
  "assay_construct_start": 1,
  "assay_record_id": "PWWP11:ASSAY:0008",
  "assay_type": "SPR apparent Kd",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": null,
  "baseline_assay_record": 0,
  "baseline_original": null,
  "buffer": "50 mM Tris-HCl, 150 mM NaCl, 0.05% Tween 20",
  "ccd_id": null,
  "ccd_mapping_source": null,
  "chemical_id": null,
  "chemical_identity_status": "named_macromolecule_no_full_sequence_identity",
  "component_context": null,
  "compound_name": "NbH10",
  "conditions": "{\"protein_construct\": \"PSIP1 1\u201390\", \"replicates\": 3, \"uncertainty_type\": \"SD\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:O75475:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Table 1 NbH10 column; SPR methods",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13204740/",
  "gene": "PSIP1",
  "interpretation": "Apparent SPR affinity of a nanobody; not a small molecule or a solved nanobody\u2013PWWP complex.",
  "molecular_entity_type": "nanobody",
  "numeric_transcription_status": "matches_primary_table",
  "numeric_value_inferred_from_structure": null,
  "pH": 7.4,
  "pdb_id": null,
  "preparation_id": "PREP:NbH10",
  "protein_id": "UP:O75475",
  "qualitative_result": null,
  "reference_id": "PMID:42194065",
  "remaining_uncertainty": null,
  "replicates": "3",
  "role": "macromolecular_binder",
  "source_component_url": null,
  "source_id": "S06",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "local_primary_full_text_XML_table_and_methods_verified",
  "temperature_C": 25,
  "uncertainty": 9.1,
  "uncertainty_type": "SD",
  "uncertainty_uM": 0.0091,
  "unit_conversion": null,
  "units": "nM",
  "value": 94.4,
  "value_operator": "=",
  "value_uM": 0.0944,
  "verification_level": null
}

NSD3 PWWP1 · source-specific experiments

Reported observations for Domain B

Export CSV
PreparationTested target & constructMethod / endpointOriginal observationConditions & uncertaintySource & verification
BI-9321PREP:BI-9321 NSD3 PWWP1
263–398Homo sapiens		 KdSPR Kddirect binding affinity = 166 ± 3 nM0.166 µM · exact unit conversion
Experimental context
Replicates
3 independent experiments (Figure 3a); 4 (Supplementary Table 7); unresolved source discrepancy
Uncertainty definition
SD
Temperature
—
Buffer
50 mM Tris; 150 mM NaCl; 1 mM TCEP; 0.005% Tween-20; 2% DMSO
Conditions
{}
Qualification
Primary replicate conflict: Figure 3a states n=3 independent experiments, while Supplementary Table 7 states SPR n=4; both report SD. Indexed primary SPR Methods supply residues 263–398 and buffer, but the full PDF was unavailable. Exact assay temperature, mutations and per-dose contact times remain not inspected.
 PMID:31285596 · 2019Phase 3 actual publisher Supplementary Table 7 and official Figure 3/4 captions; selected indexed accepted-manuscript Methods, full PDF unavailable (403); developer identity page
Original observation record
{
  "DMSO_percent": 2.0,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": 398,
  "assay_construct_start": 263,
  "assay_record_id": "PWWP:ASSAY:0008",
  "assay_type": "SPR Kd",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": "retain_with_explicit_endpoint_and_identity",
  "baseline_assay_record": 1,
  "baseline_original": "{\"assay_record_id\": \"PWWP:ASSAY:0008\", \"assay_type\": \"SPR Kd\", \"ccd_id\": \"EJE\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"BI-9321\", \"conditions\": {}, \"domain\": \"PWWP1\", \"evidence_location\": \"SGC probe developer report: Overview\", \"evidence_url\": \"https://www.thesgc.org/chemical-probes/bi-9321\", \"gene\": \"NSD3\", \"interpretation\": \"Primary developer website; original full article assay table was not retrieved.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"6G2O\", \"reference_id\": \"PMID:31285596\", \"role\": \"reported_chemical_probe\", \"uncertainty\": null, \"units\": \"nM\", \"value\": 166, \"value_operator\": \"=\", \"verification_level\": \"primary_developer_assay_report_verified\"}",
  "buffer": "50 mM Tris; 150 mM NaCl; 1 mM TCEP; 0.005% Tween-20; 2% DMSO",
  "ccd_id": "EJE",
  "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json",
  "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N",
  "chemical_identity_status": "exact_single_CCD_identity",
  "component_context": null,
  "compound_name": "BI-9321",
  "conditions": "{}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "SGC probe developer report: Overview",
  "evidence_url": "https://www.thesgc.org/chemical-probes/bi-9321",
  "gene": "NSD3",
  "interpretation": "Primary developer website; original full article assay table was not retrieved.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_report",
  "numeric_value_inferred_from_structure": 0,
  "pH": 8.0,
  "pdb_id": "6G2O",
  "preparation_id": "PREP:BI-9321",
  "protein_id": "UP:Q9BZ95",
  "qualitative_result": null,
  "reference_id": "PMID:31285596",
  "remaining_uncertainty": "Primary replicate conflict: Figure 3a states n=3 independent experiments, while Supplementary Table 7 states SPR n=4; both report SD. Indexed primary SPR Methods supply residues 263\u2013398 and buffer, but the full PDF was unavailable. Exact assay temperature, mutations and per-dose contact times remain not inspected.",
  "replicates": "3 independent experiments (Figure 3a); 4 (Supplementary Table 7); unresolved source discrepancy",
  "role": "reported_chemical_probe",
  "source_component_url": null,
  "source_id": "S03",
  "source_reported_uncertainty": "3.0",
  "source_reported_units": "nM",
  "source_reported_value": "166",
  "source_verification_scope": "Phase 3 actual publisher Supplementary Table 7 and official Figure 3/4 captions; selected indexed accepted-manuscript Methods, full PDF unavailable (403); developer identity page",
  "temperature_C": null,
  "uncertainty": 3.0,
  "uncertainty_type": "SD",
  "uncertainty_uM": 0.003,
  "unit_conversion": null,
  "units": "nM",
  "value": 166.0,
  "value_operator": "=",
  "value_uM": 0.166,
  "verification_level": "primary_developer_assay_report_verified"
}
BI-9321PREP:BI-9321 NSD3 PWWP1
Construct not curatedHomo sapiens		 IC50NanoBRET IC50cellular interaction response = 1.2 ± 0.06 µM1.2 µM · exact unit conversion
Experimental context
Replicates
3 independent replicates (Figure 4e; also Supplementary Table 7)
Uncertainty definition
SD
Temperature
—
Buffer
Not curated
Conditions
{"cell_line": "U2OS"}
Qualification
The value 1.2 ± 0.06 uM, SD and n=3 were verified in the actual Supplementary Table 7. Full NanoBRET construct and conditions were not inspected. The 1.4 uM direct tracer-engagement endpoint is separate from this histone PPI assay.
 PMID:31285596 · 2019Phase 3 actual publisher Supplementary Table 7 and official Figure 3/4 captions; selected indexed accepted-manuscript Methods, full PDF unavailable (403); developer identity page
Original observation record
{
  "DMSO_percent": null,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": null,
  "assay_construct_start": null,
  "assay_record_id": "PWWP:ASSAY:0009",
  "assay_type": "NanoBRET IC50",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": "retain_with_explicit_endpoint_and_identity",
  "baseline_assay_record": 1,
  "baseline_original": "{\"assay_record_id\": \"PWWP:ASSAY:0009\", \"assay_type\": \"NanoBRET IC50\", \"ccd_id\": \"EJE\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"BI-9321\", \"conditions\": {\"cell_line\": \"U2OS\"}, \"domain\": \"PWWP1\", \"evidence_location\": \"SGC probe developer report: Overview\", \"evidence_url\": \"https://www.thesgc.org/chemical-probes/bi-9321\", \"gene\": \"NSD3\", \"interpretation\": \"\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"6G2O\", \"reference_id\": \"PMID:31285596\", \"role\": \"reported_chemical_probe\", \"uncertainty\": null, \"units\": \"\u00b5M\", \"value\": 1.2, \"value_operator\": \"=\", \"verification_level\": \"primary_developer_assay_report_verified\"}",
  "buffer": null,
  "ccd_id": "EJE",
  "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json",
  "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N",
  "chemical_identity_status": "exact_single_CCD_identity",
  "component_context": null,
  "compound_name": "BI-9321",
  "conditions": "{\"cell_line\": \"U2OS\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "cellular_interaction_response",
  "evidence_location": "SGC probe developer report: Overview",
  "evidence_url": "https://www.thesgc.org/chemical-probes/bi-9321",
  "gene": "NSD3",
  "interpretation": null,
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_report",
  "numeric_value_inferred_from_structure": 0,
  "pH": null,
  "pdb_id": "6G2O",
  "preparation_id": "PREP:BI-9321",
  "protein_id": "UP:Q9BZ95",
  "qualitative_result": null,
  "reference_id": "PMID:31285596",
  "remaining_uncertainty": "The value 1.2 \u00b1 0.06 uM, SD and n=3 were verified in the actual Supplementary Table 7. Full NanoBRET construct and conditions were not inspected. The 1.4 uM direct tracer-engagement endpoint is separate from this histone PPI assay.",
  "replicates": "3 independent replicates (Figure 4e; also Supplementary Table 7)",
  "role": "reported_chemical_probe",
  "source_component_url": null,
  "source_id": "S03",
  "source_reported_uncertainty": "0.06",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "1.2",
  "source_verification_scope": "Phase 3 actual publisher Supplementary Table 7 and official Figure 3/4 captions; selected indexed accepted-manuscript Methods, full PDF unavailable (403); developer identity page",
  "temperature_C": null,
  "uncertainty": 0.06,
  "uncertainty_type": "SD",
  "uncertainty_uM": 0.06,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 1.2,
  "value_operator": "=",
  "value_uM": 1.2,
  "verification_level": "primary_developer_assay_report_verified"
}
BI-9321PREP:BI-9321 NSD3 PWWP1
247–402Homo sapiens		 KdITC Kddirect binding affinity = 1.7 ± 0.04 µM1.7 µM · exact unit conversion
Experimental context
Replicates
2 independent measurements
Uncertainty definition
SD
Temperature
15 °C
Buffer
50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP
Conditions
{'buffer': '50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP', 'compound_syringe_concentration_uM': 200, 'construct': 'NSD3 247–402 in pNICBio2, E. coli expressed', 'first_injection_removed': True, 'model': 'single binding site', 'pH': 6.8, 'protein_concentration_uM': 20, 'temperature_C': 15}
Qualification
Primary manuscript and Methods inspected; individual raw titration files not re-fitted. BI-9321 is a distinct study-specific ITC measurement, not the original 2019 SPR result.
 PMID:34469831 · 2022NCBI BioC primary full text; Results, ITC Methods and Figure 2/3 captions inspected
Original observation record
{
  "DMSO_percent": 1,
  "assay_construct_end": 402,
  "assay_construct_start": 247,
  "assay_context": "purified_domain",
  "assay_organism": "Homo sapiens",
  "assay_record_id": "PWWP5:ASSAY:0001",
  "assay_type": "ITC Kd",
  "assay_value_transferred_to_modeled_stereoisomers": false,
  "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP",
  "ccd_id": null,
  "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N",
  "compound_name": "BI-9321",
  "conditions": {
    "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP",
    "compound_syringe_concentration_uM": 200,
    "construct": "NSD3 247\u2013402 in pNICBio2, E. coli expressed",
    "first_injection_removed": true,
    "model": "single binding site",
    "pH": 6.8,
    "protein_concentration_uM": 20,
    "temperature_C": 15
  },
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint": "Kd",
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Results and Figure 2B-D; STAR Methods: ITC",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8882712/",
  "gene": "NSD3",
  "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.",
  "is_negative": false,
  "numeric_transcription_status": "source_preserved",
  "numeric_value_inferred_from_structure": false,
  "pH": 6.8,
  "pdb_id": null,
  "preparation_id": "PREP:BI-9321",
  "protein_id": "UP:Q9BZ95",
  "publication_year": 2022,
  "reference_id": "PMID:34469831",
  "remaining_uncertainty": "Primary manuscript and Methods inspected; individual raw titration files not re-fitted. BI-9321 is a distinct study-specific ITC measurement, not the original 2019 SPR result.",
  "replicates": "2 independent measurements",
  "retrieval_date": "2026-10-26",
  "role": "experimentally_studied_ligand",
  "source_id": "P5:S:XU2022",
  "source_reported_uncertainty": "0.04",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "1.7",
  "source_verification_scope": "NCBI BioC primary full text; Results, ITC Methods and Figure 2/3 captions inspected",
  "temperature_C": 15,
  "uncertainty": 0.04,
  "uncertainty_type": "SD",
  "uncertainty_uM": 0.04,
  "units": "\u00b5M",
  "value": 1.7,
  "value_operator": "=",
  "value_uM": 1.7,
  "verification_level": "primary_source_verified",
  "version": "phase5.chemical_curation.1.1.0"
}
BI-9466PREP:BI-9466 NSD3 PWWP1
Construct not curatedHomo sapiens		 qualitativeOfficial SGC control activity summaryqualitative control SGC reports approximately 200-fold lower activity than BI-9321 and designates it the matched negative control.
Experimental context
Replicates
Not curated
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
°C
Buffer
Not curated
Conditions
Not curated
Qualification
Endpoint-specific absolute numeric value and test construct not transcribed; no numerical affinity derived from the fold statement.
 P5:S:SGC_BI9321Official SGC probe page; explicit BI-9466 SMILES, InChI and InChIKey corroborated against PubChem
Original observation record
{
  "assay_construct_end": null,
  "assay_construct_start": null,
  "assay_context": "purified_domain",
  "assay_organism": "Homo sapiens",
  "assay_record_id": "PWWP5:ASSAY:0008",
  "assay_type": "Official SGC control activity summary",
  "assay_value_transferred_to_modeled_stereoisomers": false,
  "ccd_id": null,
  "chemical_id": "INCHIKEY:SFZHMKDAVPIXRB-UHFFFAOYSA-N",
  "compound_name": "BI-9466",
  "conditions": {},
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint": "qualitative",
  "evidence_class": "qualitative_control",
  "evidence_location": "Overview",
  "evidence_url": "https://www.thesgc.org/chemical-probes/bi-9321",
  "gene": "NSD3",
  "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.",
  "is_negative": false,
  "negative_control_scope": "Weaker NSD3-PWWP1 antagonist; use matched dose response per source",
  "numeric_transcription_status": "qualitative_or_not_reported",
  "numeric_value_inferred_from_structure": false,
  "pdb_id": null,
  "preparation_id": "PREP:BI-9466",
  "protein_id": "UP:Q9BZ95",
  "publication_year": null,
  "qualitative_result": "SGC reports approximately 200-fold lower activity than BI-9321 and designates it the matched negative control.",
  "reference_id": "P5:S:SGC_BI9321",
  "remaining_uncertainty": "Endpoint-specific absolute numeric value and test construct not transcribed; no numerical affinity derived from the fold statement.",
  "replicates": null,
  "retrieval_date": "2026-10-26",
  "role": "negative_control",
  "source_id": "P5:S:SGC_BI9321",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Official SGC probe page; explicit BI-9466 SMILES, InChI and InChIKey corroborated against PubChem",
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "units": null,
  "value": null,
  "value_operator": null,
  "value_uM": null,
  "verification_level": "official_probe_resource_verified",
  "version": "phase5.chemical_curation.1.1.0"
}
compound 11 (Collie 2025)PREP:COLLIE2025_11Negative / censored NSD3 PWWP1
263–398Homo sapiens		 KdSPR Kd counter-screennegative binding test No binding
Experimental context
Replicates
at least 3 independent replicates (Table 1 general SPR definition)
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
25 °C
Buffer
10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO
Conditions
{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}
Qualification
Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.
 PMID:40959233 · 2025Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected
Original observation record
{
  "DMSO_percent": 0.3,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": 398,
  "assay_construct_start": 263,
  "assay_record_id": "PWWP11:ASSAY:0005",
  "assay_type": "SPR Kd counter-screen",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": null,
  "baseline_assay_record": 0,
  "baseline_original": null,
  "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO",
  "ccd_id": null,
  "ccd_mapping_source": null,
  "chemical_id": null,
  "chemical_identity_status": "assayed_stereoisomeric_mixture_not_single_chemical_identity",
  "component_context": null,
  "compound_name": "compound 11 (Collie 2025)",
  "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263\u2013398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "negative_binding_test",
  "evidence_location": "Table 1 NSD3 (263\u2013398) column",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/",
  "gene": "NSD3",
  "interpretation": "Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_table",
  "numeric_value_inferred_from_structure": null,
  "pH": 7.5,
  "pdb_id": null,
  "preparation_id": "PREP:COLLIE2025_11",
  "protein_id": "UP:Q9BZ95",
  "qualitative_result": "No binding",
  "reference_id": "PMID:40959233",
  "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.",
  "replicates": "at least 3 independent replicates (Table 1 general SPR definition)",
  "role": "counter_target_assay",
  "source_component_url": null,
  "source_id": "S05",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected",
  "temperature_C": 25,
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "unit_conversion": null,
  "units": null,
  "value": null,
  "value_operator": null,
  "value_uM": null,
  "verification_level": null
}
compound 12 (Collie 2025)PREP:COLLIE2025_12Negative / censored NSD3 PWWP1
263–398Homo sapiens		 KdSPR Kd counter-screennegative binding test No binding
Experimental context
Replicates
at least 3 independent replicates (Table 1 general SPR definition)
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
25 °C
Buffer
10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO
Conditions
{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}
Qualification
Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.
 PMID:40959233 · 2025Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected
Original observation record
{
  "DMSO_percent": 0.3,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": 398,
  "assay_construct_start": 263,
  "assay_record_id": "PWWP11:ASSAY:0006",
  "assay_type": "SPR Kd counter-screen",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": null,
  "baseline_assay_record": 0,
  "baseline_original": null,
  "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO",
  "ccd_id": null,
  "ccd_mapping_source": null,
  "chemical_id": null,
  "chemical_identity_status": "paper_label_exact_identity_unresolved",
  "component_context": null,
  "compound_name": "compound 12 (Collie 2025)",
  "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263\u2013398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "negative_binding_test",
  "evidence_location": "Table 1 NSD3 (263\u2013398) column",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/",
  "gene": "NSD3",
  "interpretation": "Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_table",
  "numeric_value_inferred_from_structure": null,
  "pH": 7.5,
  "pdb_id": null,
  "preparation_id": "PREP:COLLIE2025_12",
  "protein_id": "UP:Q9BZ95",
  "qualitative_result": "No binding",
  "reference_id": "PMID:40959233",
  "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.",
  "replicates": "at least 3 independent replicates (Table 1 general SPR definition)",
  "role": "counter_target_assay",
  "source_component_url": null,
  "source_id": "S05",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected",
  "temperature_C": 25,
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "unit_conversion": null,
  "units": null,
  "value": null,
  "value_operator": null,
  "value_uM": null,
  "verification_level": null
}
compound 13 (Collie 2025)PREP:COLLIE2025_13Negative / censored NSD3 PWWP1
263–398Homo sapiens		 KdSPR Kd counter-screennegative binding test No binding
Experimental context
Replicates
at least 3 independent replicates (Table 1 general SPR definition)
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
25 °C
Buffer
10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO
Conditions
{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}
Qualification
Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.
 PMID:40959233 · 2025Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected
Original observation record
{
  "DMSO_percent": 0.3,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": 398,
  "assay_construct_start": 263,
  "assay_record_id": "PWWP11:ASSAY:0007",
  "assay_type": "SPR Kd counter-screen",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": null,
  "baseline_assay_record": 0,
  "baseline_original": null,
  "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO",
  "ccd_id": null,
  "ccd_mapping_source": null,
  "chemical_id": null,
  "chemical_identity_status": "paper_label_exact_identity_unresolved",
  "component_context": null,
  "compound_name": "compound 13 (Collie 2025)",
  "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263\u2013398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "negative_binding_test",
  "evidence_location": "Table 1 NSD3 (263\u2013398) column",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/",
  "gene": "NSD3",
  "interpretation": "Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_table",
  "numeric_value_inferred_from_structure": null,
  "pH": 7.5,
  "pdb_id": null,
  "preparation_id": "PREP:COLLIE2025_13",
  "protein_id": "UP:Q9BZ95",
  "qualitative_result": "No binding",
  "reference_id": "PMID:40959233",
  "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.",
  "replicates": "at least 3 independent replicates (Table 1 general SPR definition)",
  "role": "counter_target_assay",
  "source_component_url": null,
  "source_id": "S05",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected",
  "temperature_C": 25,
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "unit_conversion": null,
  "units": null,
  "value": null,
  "value_operator": null,
  "value_uM": null,
  "verification_level": null
}
compound 5 (Collie 2025)PREP:COLLIE2025_5Negative / censored NSD3 PWWP1
263–398Homo sapiens		 KdSPR Kd counter-screencensored binding limit > 30 µM
Experimental context
Replicates
at least 3 independent replicates (Table 1 general SPR definition)
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
25 °C
Buffer
10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO
Conditions
{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}
Qualification
Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.
 PMID:40959233 · 2025Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected
Original observation record
{
  "DMSO_percent": 0.3,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": 398,
  "assay_construct_start": 263,
  "assay_record_id": "PWWP11:ASSAY:0002",
  "assay_type": "SPR Kd counter-screen",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": null,
  "baseline_assay_record": 0,
  "baseline_original": null,
  "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO",
  "ccd_id": null,
  "ccd_mapping_source": null,
  "chemical_id": null,
  "chemical_identity_status": "assayed_stereoisomeric_mixture_not_single_chemical_identity",
  "component_context": null,
  "compound_name": "compound 5 (Collie 2025)",
  "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263\u2013398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "censored_binding_limit",
  "evidence_location": "Table 1 NSD3 (263\u2013398) column",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/",
  "gene": "NSD3",
  "interpretation": "Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_table",
  "numeric_value_inferred_from_structure": null,
  "pH": 7.5,
  "pdb_id": null,
  "preparation_id": "PREP:COLLIE2025_5",
  "protein_id": "UP:Q9BZ95",
  "qualitative_result": null,
  "reference_id": "PMID:40959233",
  "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.",
  "replicates": "at least 3 independent replicates (Table 1 general SPR definition)",
  "role": "counter_target_assay",
  "source_component_url": null,
  "source_id": "S05",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected",
  "temperature_C": 25,
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 30.0,
  "value_operator": "\u003e",
  "value_uM": 30.0,
  "verification_level": null
}
compound 6 (Collie 2025)PREP:COLLIE2025_6Negative / censored NSD3 PWWP1
263–398Homo sapiens		 KdSPR Kd counter-screencensored binding limit > 30 µM
Experimental context
Replicates
at least 3 independent replicates (Table 1 general SPR definition)
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
25 °C
Buffer
10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO
Conditions
{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}
Qualification
Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.
 PMID:40959233 · 2025Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected
Original observation record
{
  "DMSO_percent": 0.3,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": 398,
  "assay_construct_start": 263,
  "assay_record_id": "PWWP11:ASSAY:0003",
  "assay_type": "SPR Kd counter-screen",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": null,
  "baseline_assay_record": 0,
  "baseline_original": null,
  "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO",
  "ccd_id": null,
  "ccd_mapping_source": null,
  "chemical_id": null,
  "chemical_identity_status": "paper_label_exact_identity_unresolved",
  "component_context": null,
  "compound_name": "compound 6 (Collie 2025)",
  "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263\u2013398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "censored_binding_limit",
  "evidence_location": "Table 1 NSD3 (263\u2013398) column",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/",
  "gene": "NSD3",
  "interpretation": "Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_table",
  "numeric_value_inferred_from_structure": null,
  "pH": 7.5,
  "pdb_id": null,
  "preparation_id": "PREP:COLLIE2025_6",
  "protein_id": "UP:Q9BZ95",
  "qualitative_result": null,
  "reference_id": "PMID:40959233",
  "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.",
  "replicates": "at least 3 independent replicates (Table 1 general SPR definition)",
  "role": "counter_target_assay",
  "source_component_url": null,
  "source_id": "S05",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected",
  "temperature_C": 25,
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 30.0,
  "value_operator": "\u003e",
  "value_uM": 30.0,
  "verification_level": null
}
compound 7 (Collie 2025)PREP:COLLIE2025_7Negative / censored NSD3 PWWP1
263–398Homo sapiens		 KdSPR Kd counter-screencensored binding limit > 30 µM
Experimental context
Replicates
at least 3 independent replicates (Table 1 general SPR definition)
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
25 °C
Buffer
10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO
Conditions
{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}
Qualification
Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.
 PMID:40959233 · 2025Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected
Original observation record
{
  "DMSO_percent": 0.3,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": 398,
  "assay_construct_start": 263,
  "assay_record_id": "PWWP11:ASSAY:0004",
  "assay_type": "SPR Kd counter-screen",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": null,
  "baseline_assay_record": 0,
  "baseline_original": null,
  "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO",
  "ccd_id": "A1IEF",
  "ccd_mapping_source": null,
  "chemical_id": "INCHIKEY:HHACEXLLNHJLFT-INIZCTEOSA-N",
  "chemical_identity_status": "exact_single_CCD_identity",
  "component_context": null,
  "compound_name": "compound 7 (Collie 2025)",
  "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263\u2013398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "censored_binding_limit",
  "evidence_location": "Table 1 NSD3 (263\u2013398) column",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/",
  "gene": "NSD3",
  "interpretation": "Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_table",
  "numeric_value_inferred_from_structure": null,
  "pH": 7.5,
  "pdb_id": null,
  "preparation_id": "PREP:COLLIE2025_7",
  "protein_id": "UP:Q9BZ95",
  "qualitative_result": null,
  "reference_id": "PMID:40959233",
  "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.",
  "replicates": "at least 3 independent replicates (Table 1 general SPR definition)",
  "role": "counter_target_assay",
  "source_component_url": null,
  "source_id": "S05",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected",
  "temperature_C": 25,
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 30.0,
  "value_operator": "\u003e",
  "value_uM": 30.0,
  "verification_level": null
}
MS9715PREP:MS9715 NSD3 PWWP1
247–402Homo sapiens		 KdITC Kddirect binding affinity = 1.3 ± 0.17 µM1.3 µM · exact unit conversion
Experimental context
Replicates
2 independent measurements
Uncertainty definition
SD
Temperature
15 °C
Buffer
50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP
Conditions
{'buffer': '50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP', 'compound_syringe_concentration_uM': 200, 'construct': 'NSD3 247–402 in pNICBio2, E. coli expressed', 'first_injection_removed': True, 'model': 'single binding site', 'pH': 6.8, 'protein_concentration_uM': 20, 'temperature_C': 15}
Qualification
Primary manuscript and Methods inspected; individual raw titration files not re-fitted. BI-9321 is a distinct study-specific ITC measurement, not the original 2019 SPR result.
 PMID:34469831 · 2022NCBI BioC primary full text; Results, ITC Methods and Figure 2/3 captions inspected
Original observation record
{
  "DMSO_percent": 1,
  "assay_construct_end": 402,
  "assay_construct_start": 247,
  "assay_context": "purified_domain",
  "assay_organism": "Homo sapiens",
  "assay_record_id": "PWWP5:ASSAY:0002",
  "assay_type": "ITC Kd",
  "assay_value_transferred_to_modeled_stereoisomers": false,
  "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP",
  "ccd_id": null,
  "chemical_id": "INCHIKEY:RWXCSOWWDBANDF-LPFSXYLXSA-N",
  "compound_name": "MS9715",
  "conditions": {
    "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP",
    "compound_syringe_concentration_uM": 200,
    "construct": "NSD3 247\u2013402 in pNICBio2, E. coli expressed",
    "first_injection_removed": true,
    "model": "single binding site",
    "pH": 6.8,
    "protein_concentration_uM": 20,
    "temperature_C": 15
  },
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint": "Kd",
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Results and Figure 2B-D; STAR Methods: ITC",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8882712/",
  "gene": "NSD3",
  "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.",
  "is_negative": false,
  "numeric_transcription_status": "source_preserved",
  "numeric_value_inferred_from_structure": false,
  "pH": 6.8,
  "pdb_id": null,
  "preparation_id": "PREP:MS9715",
  "protein_id": "UP:Q9BZ95",
  "publication_year": 2022,
  "reference_id": "PMID:34469831",
  "remaining_uncertainty": "Primary manuscript and Methods inspected; individual raw titration files not re-fitted. BI-9321 is a distinct study-specific ITC measurement, not the original 2019 SPR result.",
  "replicates": "2 independent measurements",
  "retrieval_date": "2026-10-26",
  "role": "reported_degrader",
  "source_id": "P5:S:XU2022",
  "source_reported_uncertainty": "0.17",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "1.3",
  "source_verification_scope": "NCBI BioC primary full text; Results, ITC Methods and Figure 2/3 captions inspected",
  "temperature_C": 15,
  "uncertainty": 0.17,
  "uncertainty_type": "SD",
  "uncertainty_uM": 0.17,
  "units": "\u00b5M",
  "value": 1.3,
  "value_operator": "=",
  "value_uM": 1.3,
  "verification_level": "primary_source_verified",
  "version": "phase5.chemical_curation.1.1.0"
}
MS9715NPREP:MS9715N NSD3 PWWP1
247–402Homo sapiens		 KdITC Kddirect binding affinity = 1.62 ± 0.33 µM1.62 µM · exact unit conversion
Experimental context
Replicates
2 independent measurements
Uncertainty definition
SD
Temperature
15 °C
Buffer
50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP
Conditions
{'buffer': '50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP', 'compound_syringe_concentration_uM': 200, 'construct': 'NSD3 247–402 in pNICBio2, E. coli expressed', 'first_injection_removed': True, 'model': 'single binding site', 'pH': 6.8, 'protein_concentration_uM': 20, 'temperature_C': 15}
Qualification
Primary manuscript and Methods inspected; individual raw titration files not re-fitted. BI-9321 is a distinct study-specific ITC measurement, not the original 2019 SPR result.
 PMID:34469831 · 2022NCBI BioC primary full text; Results, ITC Methods and Figure 2/3 captions inspected
Original observation record
{
  "DMSO_percent": 1,
  "assay_construct_end": 402,
  "assay_construct_start": 247,
  "assay_context": "purified_domain",
  "assay_organism": "Homo sapiens",
  "assay_record_id": "PWWP5:ASSAY:0003",
  "assay_type": "ITC Kd",
  "assay_value_transferred_to_modeled_stereoisomers": false,
  "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP",
  "ccd_id": null,
  "chemical_id": null,
  "compound_name": "MS9715N",
  "conditions": {
    "buffer": "50 mM Tris-HCl; 150 mM NaCl; 1% DMSO; 3% NMP",
    "compound_syringe_concentration_uM": 200,
    "construct": "NSD3 247\u2013402 in pNICBio2, E. coli expressed",
    "first_injection_removed": true,
    "model": "single binding site",
    "pH": 6.8,
    "protein_concentration_uM": 20,
    "temperature_C": 15
  },
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint": "Kd",
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Results and Figure 2B-D; STAR Methods: ITC",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8882712/",
  "gene": "NSD3",
  "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.",
  "is_negative": false,
  "numeric_transcription_status": "source_preserved",
  "numeric_value_inferred_from_structure": false,
  "pH": 6.8,
  "pdb_id": null,
  "preparation_id": "PREP:MS9715N",
  "protein_id": "UP:Q9BZ95",
  "publication_year": 2022,
  "reference_id": "PMID:34469831",
  "remaining_uncertainty": "Primary manuscript and Methods inspected; individual raw titration files not re-fitted. BI-9321 is a distinct study-specific ITC measurement, not the original 2019 SPR result.",
  "replicates": "2 independent measurements",
  "retrieval_date": "2026-10-26",
  "role": "negative_control",
  "source_id": "P5:S:XU2022",
  "source_reported_uncertainty": "0.33",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "1.62",
  "source_verification_scope": "NCBI BioC primary full text; Results, ITC Methods and Figure 2/3 captions inspected",
  "temperature_C": 15,
  "uncertainty": 0.33,
  "uncertainty_type": "SD",
  "uncertainty_uM": 0.33,
  "units": "\u00b5M",
  "value": 1.62,
  "value_operator": "=",
  "value_uM": 1.62,
  "verification_level": "primary_source_verified",
  "version": "phase5.chemical_curation.1.1.0"
}
UNC6934PREP:UNC6934Negative / censored NSD3 PWWP1
263–398Homo sapiens		 KdSPR Kd counter-screencensored binding limit > 30 µM
Experimental context
Replicates
at least 3 independent replicates (Table 1 general SPR definition)
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
25 °C
Buffer
10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO
Conditions
{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD3 263–398", "purified_tags": "N-terminal 6His-TEV retained"}
Qualification
Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.
 PMID:40959233 · 2025Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected
Original observation record
{
  "DMSO_percent": 0.3,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": 398,
  "assay_construct_start": 263,
  "assay_record_id": "PWWP11:ASSAY:0001",
  "assay_type": "SPR Kd counter-screen",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": null,
  "baseline_assay_record": 0,
  "baseline_original": null,
  "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.1 mM TCEP; 0.05% (w/v) Tween-20; 0.3% (v/v) DMSO",
  "ccd_id": "V01",
  "ccd_mapping_source": null,
  "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N",
  "chemical_identity_status": "exact_single_CCD_identity",
  "component_context": null,
  "compound_name": "UNC6934",
  "conditions": "{\"assay_substitutions\": \"not listed for assay constructs; 9FOE crystallographic mutants kept separate\", \"phase3_verification\": \"SV05A/SV05B\", \"protein_construct\": \"NSD3 263\u2013398\", \"purified_tags\": \"N-terminal 6His-TEV retained\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:Q9BZ95:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "censored_binding_limit",
  "evidence_location": "Table 1 NSD3 (263\u2013398) column",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/",
  "gene": "NSD3",
  "interpretation": "Single counter-target experiment; not evidence of proteome-wide selectivity. No-binding rows have no inferred numerical threshold.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_table",
  "numeric_value_inferred_from_structure": null,
  "pH": 7.5,
  "pdb_id": null,
  "preparation_id": "PREP:UNC6934",
  "protein_id": "UP:Q9BZ95",
  "qualitative_result": null,
  "reference_id": "PMID:40959233",
  "remaining_uncertainty": "Assay-specific buffer and temperature verified from SI page 9; tag/construct from Table S2. Exact per-row kinetic-versus-steady-state fit choice and exact n beyond table footnote not specified. Chemical preparation identity remains as curated.",
  "replicates": "at least 3 independent replicates (Table 1 general SPR definition)",
  "role": "counter_target_assay",
  "source_component_url": null,
  "source_id": "S05",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Phase 3 primary Table 1 and actual supporting PDF pages 7, 9 and 14; the inherited HTRF method remains explicitly not inspected",
  "temperature_C": 25,
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 30.0,
  "value_operator": "\u003e",
  "value_uM": 30.0,
  "verification_level": null
}