PWWPAtlas
STRUCTURAL BIOLOGY & CHEMICAL EVIDENCEDataset v1.2 · Phase 6D · Comparative experimental recognition environments
Verified 2D molecular structure of BI-9466 Verified 2D molecular structure of BI-9466

Resolved chemical identity

BI-9466

Studied · no deposited PWWP research ligandExperimental control

Neutral parent/reference identity shown separately from the experimentally assayed preparation; salt, solvent and lot composition not independently established.

NSD3 PWWP1
1 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

Stable identity
INCHIKEY:SFZHMKDAVPIXRB-UHFFFAOYSA-N
Full InChIKey
SFZHMKDAVPIXRB-UHFFFAOYSA-N
Source identity status
resolved reference identity
Deposited CCD identifiers
No exact CCD mapping curated
External identifiers
PubChem CID: 138115340
Reference formula
C17H21N5
Calculated molecular weight
295.39
Calculated descriptors
cLogP 2.5631 · TPSA 61.66 Ų · HBD 1 · HBA 5RDKit 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
CC1=CC(=CC(=C1C2=C(N(C=N2)C)C3=CN=CN3C)C)CN
InChI
InChI=1S/C17H21N5/c1-11-5-13(7-18)6-12(2)15(11)16-17(22(4)10-20-16)14-8-19-9-21(14)3/h5-6,8-10H,7,18H2,1-4H3
{
  "aliases": [],
  "bound_pose": false,
  "canonical_smiles": "CC1=CC(=CC(=C1C2=C(N(C=N2)C)C3=CN=CN3C)C)CN",
  "ccd_ids": [],
  "chemical_id": "INCHIKEY:SFZHMKDAVPIXRB-UHFFFAOYSA-N",
  "clinical_status": "not independently assessed",
  "curation_version": "phase5-1.0.0",
  "external_identifiers": {
    "PubChem CID": "138115340"
  },
  "identity_status": "resolved_reference_identity",
  "identity_verification": "Exact SGC SMILES/InChI/InChIKey matched PubChem neutral identity; hydrochloride retained as a separate salt identity",
  "inchi": "InChI=1S/C17H21N5/c1-11-5-13(7-18)6-12(2)15(11)16-17(22(4)10-20-16)14-8-19-9-21(14)3/h5-6,8-10H,7,18H2,1-4H3",
  "inchikey": "SFZHMKDAVPIXRB-UHFFFAOYSA-N",
  "isomeric_smiles": "CC1=CC(=CC(=C1C2=C(N(C=N2)C)C3=CN=CN3C)C)CN",
  "molecular_formula": "C17H21N5",
  "molecular_weight": "295.4",
  "name": "BI-9466",
  "primary_name": "BI-9466",
  "pubchem_cid": "138115340",
  "retrieval_date": "2026-10-26",
  "smiles": "CC1=CC(=CC(=C1C2=C(N(C=N2)C)C3=CN=CN3C)C)CN",
  "source_url": "https://pubchem.ncbi.nlm.nih.gov/compound/138115340",
  "source_urls": [
    "https://pubchem.ncbi.nlm.nih.gov/compound/138115340"
  ],
  "version": "phase5.chemical_curation.1.1.0"
}

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
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"
}

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

BI-9466

PREP:BI-9466

Neutral parent/reference identity shown separately from the experimentally assayed preparation; salt, solvent and lot composition not independently established.

negative control
Complete preparation record
{
  "chemical_id": "INCHIKEY:SFZHMKDAVPIXRB-UHFFFAOYSA-N",
  "clinical_status": "not independently assessed",
  "curation_version": "phase5-1.0.0",
  "entity_type": "small_molecule_preparation",
  "identity_note": "Neutral parent/reference identity shown separately from the experimentally assayed preparation; salt, solvent and lot composition not independently established.",
  "identity_status": "resolved_reference_parent_preparation_form_unresolved",
  "molecular_entity_type": "small_molecule_preparation",
  "name": "BI-9466",
  "phase5_identity_overlay": false,
  "preparation_id": "PREP:BI-9466",
  "retrieval_date": "2026-10-26",
  "role": "negative_control",
  "source_id": "P5:S:SGC_BI9321",
  "source_url": "https://www.thesgc.org/chemical-probes/bi-9321",
  "version": "phase5.chemical_curation.1.1.0"
}

Source-supported relationships

RelationshipRelated identity / preparationScopeSource
has salt ofBI-9466 hydrochlorideReference hydrochloride identity only; no assay values transferred between salt and parent.Source
negative control forBI-9321weaker NSD3-PWWP1 antagonist controlSource

Provenance and reproducibility

Sources & downloads

https://pubchem.ncbi.nlm.nih.gov/compound/138115340https://www.thesgc.org/chemical-probes/bi-9321
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.