PWWPAtlas
STRUCTURAL BIOLOGY & CHEMICAL EVIDENCEDataset v1.2 · Phase 6D · Comparative experimental recognition environments
Experimental preparationIdentity not assigned

Measurements remain attached to the reported preparation.

Reported experimental preparation

compound 6 (Collie 2025)

Studied · no deposited PWWP research ligandNegative / censored observationsPreparation identity unresolved

Complete deposited identity retained; no connectivity-only or name-only merge.

NSD2 PWWP1NSD3 PWWP1
4 assay / association records1 preparations0 research-ligand PDB entries

No deposited PWWP research-ligand geometry is classified for this preparation in the selected release. Deposition of a buffer/ion is not binding evidence.

Clinical / development status: Not independently curated. A chemical probe classification does not imply medicinal approval.

Identity is separate from preparation

Chemical identity

Measured target and original context

Bioactivity & experimental observations

Download assay CSV

Each row is one source-specific observation. Repeated measurements of this compound are not independent compounds. Direct binding, functional displacement and cellular outcomes retain their distinct endpoints.

PreparationTested target & constructMethod / endpointOriginal observationConditions & uncertaintySource & verification
compound 6 (Collie 2025)PREP:COLLIE2025_6 NSD2 PWWP1
208–368Homo sapiens		 KdSPR Kddirect binding affinity = 0.71 ± 0.09 µM0.71 µM · exact unit conversion
Experimental context
Replicates
at least 3 independent replicates (Table 1 general SPR definition)
Uncertainty definition
SD
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": "NSD2 208–368", "purified_tags": "N-terminal Avi; C-terminal 6His; biotinylated", "replicates": "at least 3", "uncertainty_type": "SD"}
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": 368,
  "assay_construct_start": 208,
  "assay_record_id": "PWWP:ASSAY:0016",
  "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:0016\", \"assay_type\": \"SPR Kd\", \"ccd_id\": null, \"compound_name\": \"compound 6 (Collie 2025)\", \"conditions\": {\"protein_construct\": \"NSD2 208\u2013368\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}, \"domain\": \"PWWP1\", \"evidence_location\": \"Table 1\", \"evidence_url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/\", \"gene\": \"NSD2\", \"interpretation\": \"Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": null, \"reference_id\": \"PMID:40959233\", \"role\": \"experimentally_studied_ligand\", \"uncertainty\": 0.09, \"units\": \"\u00b5M\", \"value\": 0.71, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}",
  "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\": \"NSD2 208\u2013368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:O96028:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Table 1",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/",
  "gene": "NSD2",
  "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_report",
  "numeric_value_inferred_from_structure": 0,
  "pH": 7.5,
  "pdb_id": null,
  "preparation_id": "PREP:COLLIE2025_6",
  "protein_id": "UP:O96028",
  "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": "experimentally_studied_ligand",
  "source_component_url": null,
  "source_id": "S05",
  "source_reported_uncertainty": "0.09",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "0.71",
  "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": 0.09,
  "uncertainty_type": "SD",
  "uncertainty_uM": 0.09,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 0.71,
  "value_operator": "=",
  "value_uM": 0.71,
  "verification_level": "primary_full_text_sections_verified"
}
compound 6 (Collie 2025)PREP:COLLIE2025_6 NSD2 PWWP1
211–350Homo sapiens		 KdSPR Kddirect binding affinity = 5.83 ± 0.64 µM5.83 µM · exact unit conversion
Experimental context
Replicates
at least 3 independent replicates (Table 1 general SPR definition)
Uncertainty definition
SD
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": "NSD2 211–350", "purified_tags": "N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal", "replicates": "at least 3", "uncertainty_type": "SD"}
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": 350,
  "assay_construct_start": 211,
  "assay_record_id": "PWWP:ASSAY:0023",
  "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:0023\", \"assay_type\": \"SPR Kd\", \"ccd_id\": null, \"compound_name\": \"compound 6 (Collie 2025)\", \"conditions\": {\"protein_construct\": \"NSD2 211\u2013350\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}, \"domain\": \"PWWP1\", \"evidence_location\": \"Table 1\", \"evidence_url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/\", \"gene\": \"NSD2\", \"interpretation\": \"Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": null, \"reference_id\": \"PMID:40959233\", \"role\": \"experimentally_studied_ligand\", \"uncertainty\": 0.64, \"units\": \"\u00b5M\", \"value\": 5.83, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}",
  "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\": \"NSD2 211\u2013350\", \"purified_tags\": \"N-terminal GS remnant; C-terminal Avi; biotinylated after GST/6His removal\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:O96028:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Table 1",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/",
  "gene": "NSD2",
  "interpretation": "Affinity pertains to assay construct; crystal mutations and boundaries are separately recorded.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_report",
  "numeric_value_inferred_from_structure": 0,
  "pH": 7.5,
  "pdb_id": null,
  "preparation_id": "PREP:COLLIE2025_6",
  "protein_id": "UP:O96028",
  "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": "experimentally_studied_ligand",
  "source_component_url": null,
  "source_id": "S05",
  "source_reported_uncertainty": "0.64",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "5.83",
  "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": 0.64,
  "uncertainty_type": "SD",
  "uncertainty_uM": 0.64,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 5.83,
  "value_operator": "=",
  "value_uM": 5.83,
  "verification_level": "primary_full_text_sections_verified"
}
compound 6 (Collie 2025)PREP:COLLIE2025_6 NSD2 PWWP1
208–368Homo sapiens		 IC50HTRF displacement IC50biochemical interaction inhibition = 1.24 ± 0.08 µM1.24 µM · exact unit conversion
Experimental context
Replicates
2
Uncertainty definition
SEM
Temperature
—
Buffer
Not curated
Conditions
{"assay_substitutions": "not listed for assay constructs; 9FOE crystallographic mutants kept separate", "phase3_verification": "SV05A/SV05B", "protein_construct": "NSD2 208–368", "purified_tags": "N-terminal Avi; C-terminal 6His; biotinylated", "replicates": 2, "uncertainty_type": "SEM"}
Qualification
HTRF full conditions are referenced to Carlino et al. 2024 DOI 10.1021/acs.jmedchem.4c00215. Its main protocol remains inaccessible after official repository checks. The actual supplement was inspected but contains no HTRF protocol. Table 1 reports SEM; independence level of HTRF replicates is not specified.
 PMID:40959233 · 2025Phase 3 primary Table 1 and actual Collie supporting PDF pages 7, 9 and 14; Carlino supporting PDF contents inspected, but the inherited main-article HTRF method remains not inspected after documented access attempts.
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": 368,
  "assay_construct_start": 208,
  "assay_record_id": "PWWP:ASSAY:0028",
  "assay_type": "HTRF displacement 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:0028\", \"assay_type\": \"HTRF displacement IC50\", \"ccd_id\": null, \"compound_name\": \"compound 6 (Collie 2025)\", \"conditions\": {\"protein_construct\": \"NSD2 208\u2013368\", \"replicates\": 2, \"uncertainty_type\": \"SEM\"}, \"domain\": \"PWWP1\", \"evidence_location\": \"Table 1\", \"evidence_url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/\", \"gene\": \"NSD2\", \"interpretation\": \"Probe displacement from the H3K36me2 binding site; not catalytic SET-domain inhibition.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": null, \"reference_id\": \"PMID:40959233\", \"role\": \"experimentally_studied_ligand\", \"uncertainty\": 0.08, \"units\": \"\u00b5M\", \"value\": 1.24, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}",
  "buffer": null,
  "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\": \"NSD2 208\u2013368\", \"purified_tags\": \"N-terminal Avi; C-terminal 6His; biotinylated\", \"replicates\": 2, \"uncertainty_type\": \"SEM\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:O96028:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "biochemical_interaction_inhibition",
  "evidence_location": "Table 1",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/",
  "gene": "NSD2",
  "interpretation": "Probe displacement from the H3K36me2 binding site; not catalytic SET-domain inhibition.",
  "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:COLLIE2025_6",
  "protein_id": "UP:O96028",
  "qualitative_result": null,
  "reference_id": "PMID:40959233",
  "remaining_uncertainty": "HTRF full conditions are referenced to Carlino et al. 2024 DOI 10.1021/acs.jmedchem.4c00215. Its main protocol remains inaccessible after official repository checks. The actual supplement was inspected but contains no HTRF protocol. Table 1 reports SEM; independence level of HTRF replicates is not specified.",
  "replicates": "2",
  "role": "experimentally_studied_ligand",
  "source_component_url": null,
  "source_id": "S05",
  "source_reported_uncertainty": "0.08",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "1.24",
  "source_verification_scope": "Phase 3 primary Table 1 and actual Collie supporting PDF pages 7, 9 and 14; Carlino supporting PDF contents inspected, but the inherited main-article HTRF method remains not inspected after documented access attempts.",
  "temperature_C": null,
  "uncertainty": 0.08,
  "uncertainty_type": "SEM",
  "uncertainty_uM": 0.08,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 1.24,
  "value_operator": "=",
  "value_uM": 1.24,
  "verification_level": "primary_full_text_sections_verified"
}
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
}

Exact deposited instances

Experimental structures

No verified exact-identity bound structure

The biochemical or cellular evidence remains fully available. No artificial pose has been assigned.

Preparations, identities and controls remain separate

Experimental context

compound 6 (Collie 2025)

PREP:COLLIE2025_6

Complete deposited identity retained; no connectivity-only or name-only merge.

assay preparation
Complete preparation record
{
  "chemical_id": null,
  "entity_type": "small_molecule_preparation",
  "exact_ccd_id": null,
  "identity_note": "Complete deposited identity retained; no connectivity-only or name-only merge.",
  "identity_status": "paper_label_exact_identity_unresolved",
  "modeled_candidate_ccd_ids": "[]",
  "modeled_candidate_chemical_ids": "[]",
  "name": "compound 6 (Collie 2025)",
  "preparation_id": "PREP:COLLIE2025_6",
  "role": "assay_preparation",
  "sequence_if_defined": null
}

Provenance and reproducibility

Sources & downloads

https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/
Download complete evidence JSONCuration methods & source receipts

Snapshot 2026-10-26 · phase5-1.0.0 · original measurements, operators, constructs and uncertainty are retained in the exports.