Resolved chemical identity

BI-9321

Studied + deposited research ligandReported chemical probe

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

3 assay / association records1 preparations1 research-ligand PDB entries

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

Identity is separate from preparation

Chemical identity

Stable identity: INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N
Full InChIKey: WOAOENGFAAUUGT-UHFFFAOYSA-N
Source identity status: complete deposited InChIKey
Deposited CCD identifiers: EJE
External identifiers: See deposited identity and source links

Reference formula: C22H21FN4
Calculated molecular weight: 360.436
Calculated descriptors: cLogP 4.5169 · TPSA 56.73 Å² · HBD 1 · HBA 4RDKit 2025.09.3; calculations for this source identity, not experimental measurements.
Depiction validation: verified smiles full inchikey match

SMILES, InChI & complete identity record

Isomeric SMILES: Cc1cc(cc(c1c2c(n(cn2)C)c3ccnc4c3ccc(c4)F)C)CN
InChI: Not curated

{
  "aliases": [
    "[4-[5-(7-fluoranylquinolin-4-yl)-1-methyl-imidazol-4-yl]-3,5-dimethyl-phenyl]methanamine"
  ],
  "ccd_ids": [
    "EJE"
  ],
  "ccd_names": "[\"[4-[5-(7-fluoranylquinolin-4-yl)-1-methyl-imidazol-4-yl]-3,5-dimethyl-phenyl]methanamine\"]",
  "ccd_types": "[\"non-polymer\"]",
  "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N",
  "connectivity_block": "WOAOENGFAAUUGT",
  "curated_source_sha256": null,
  "curation_version": "frozen-v1.2",
  "external_identifiers": {},
  "formal_charge_by_ccd": "{\"EJE\": 0}",
  "formulae": "[\"C22 H21 F N4\"]",
  "geometry_note": "CCD ideal SDF is a reference chemical geometry, not a deposited bound pose.",
  "identity_status": "complete_deposited_InChIKey",
  "inchikey": "WOAOENGFAAUUGT-UHFFFAOYSA-N",
  "inventory_origin": "v1_CCD_inventory",
  "isomeric_smiles": "Cc1cc(cc(c1c2c(n(cn2)C)c3ccnc4c3ccc(c4)F)C)CN",
  "primary_name": "[4-[5-(7-fluoranylquinolin-4-yl)-1-methyl-imidazol-4-yl]-3,5-dimethyl-phenyl]methanamine",
  "retrieval_date": "2026-10-24",
  "smiles_stereo_by_ccd": "{\"EJE\": \"Cc1cc(cc(c1c2c(n(cn2)C)c3ccnc4c3ccc(c4)F)C)CN\"}",
  "source_metadata_sha256": "{\"EJE\": \"4420a58e1e2dc7985843e11811dec4d72c963f256b3f66eda18bde5db1f66e3c\"}",
  "source_urls": [
    "https://www.rcsb.org/ligand/EJE"
  ]
}

Source aliases (2)

BI-9321
[4-[5-(7-fluoranylquinolin-4-yl)-1-methyl-imidazol-4-yl]-3,5-dimethyl-phenyl]methanamine

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.

Preparation	Tested target & construct	Method / endpoint	Original observation	Conditions & uncertainty	Source & 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" }

Preparation

Tested target & construct

Method / endpoint

Original observation

Conditions & uncertainty

Source & 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"
}

Exact deposited instances

Experimental structures

Native-core and broader Pfam proximity are distinguished from contacts elsewhere in a protein. Each action opens the actual deposited ligand instance. Geometric proximity does not supply a measured binding affinity.

Entry / ligand	Native domain & protein chain	Geometric evidence	Minimum distance	Inspect
6G2O · EJEPDB:6G2O:LIG:B:EJE:401:.	NSD3 PWWP1Protein label chain A · ligand label chain B	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.8197 Å Pfam: 2.8197 Å	View deposited instance

Preparations, identities and controls remain separate

Experimental context

BI-9321

PREP:BI-9321

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

assay preparation

Complete preparation record

{
  "chemical_id": "INCHIKEY:WOAOENGFAAUUGT-UHFFFAOYSA-N",
  "entity_type": "small_molecule_preparation",
  "exact_ccd_id": "EJE",
  "identity_note": "Complete deposited identity retained; no connectivity-only or name-only merge.",
  "identity_status": "exact_single_CCD_identity",
  "modeled_candidate_ccd_ids": "[]",
  "modeled_candidate_chemical_ids": "[]",
  "name": "BI-9321",
  "preparation_id": "PREP:BI-9321",
  "role": "assay_preparation",
  "sequence_if_defined": null
}

Source-supported relationships

Relationship	Related identity / preparation	Scope	Source
has negative control for	BI-9466	weaker NSD3-PWWP1 antagonist control	Source

Provenance and reproducibility

Sources & downloads

https://pmc.ncbi.nlm.nih.gov/articles/PMC8882712/https://www.rcsb.org/ligand/EJE https://www.thesgc.org/chemical-probes/bi-9321

Download complete evidence JSON Curation methods & source receipts

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