PWWPAtlas
STRUCTURAL BIOLOGY & CHEMICAL EVIDENCEDataset v1.2 · Phase 6D · Comparative experimental recognition environments
Verified 2D molecular structure of LLC0424 Verified 2D molecular structure of LLC0424

Resolved chemical identity

LLC0424

Studied · no deposited PWWP research ligand

Neutral parent/reference identity shown separately from the experimentally assayed preparation; salt, solvent and lot composition not independently established. PubChem structure has unspecified stereochemistry, which is preserved rather than assigned.

2 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:OHRABUZLZFHHEJ-UHFFFAOYSA-N
Full InChIKey
OHRABUZLZFHHEJ-UHFFFAOYSA-N
Source identity status
resolved reference identity
Deposited CCD identifiers
No exact CCD mapping curated
External identifiers
PubChem CID: 171663346
Reference formula
C45H41N7O9
Calculated molecular weight
823.863
Calculated descriptors
cLogP 3.8746 · TPSA 203.63 Ų · HBD 4 · HBA 10RDKit 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
C1CC1N(CC2=CC=C(C=C2)C(=O)NC3=CC=C(C=C3)C(=O)NC4CCN(CC4)C5=CC6=C(C=C5)C(=O)N(C6=O)C7CCC(=O)NC7=O)C(=O)C8=CC9=C(C=C8)NC(=O)CO9
InChI
InChI=1S/C45H41N7O9/c53-38-16-15-36(42(57)49-38)52-44(59)33-13-12-32(22-34(33)45(52)60)50-19-17-30(18-20-50)47-41(56)27-5-8-29(9-6-27)46-40(55)26-3-1-25(2-4-26)23-51(31-10-11-31)43(58)28-7-14-35-37(21-28)61-24-39(54)48-35/h1-9,12-14,21-22,30-31,36H,10-11,15-20,23-24H2,(H,46,55)(H,47,56)(H,48,54)(H,49,53,57)
{
  "aliases": [],
  "bound_pose": false,
  "canonical_smiles": "C1CC1N(CC2=CC=C(C=C2)C(=O)NC3=CC=C(C=C3)C(=O)NC4CCN(CC4)C5=CC6=C(C=C5)C(=O)N(C6=O)C7CCC(=O)NC7=O)C(=O)C8=CC9=C(C=C8)NC(=O)CO9",
  "ccd_ids": [],
  "chemical_id": "INCHIKEY:OHRABUZLZFHHEJ-UHFFFAOYSA-N",
  "clinical_status": "not independently assessed",
  "curation_version": "phase5-1.0.0",
  "external_identifiers": {
    "PubChem CID": "171663346"
  },
  "identity_status": "resolved_reference_identity",
  "identity_verification": "PubChem reference identity for named compound10l; primary article confirms compound10l alias and chemical synthesis; unspecified stereochemistry retained",
  "inchi": "InChI=1S/C45H41N7O9/c53-38-16-15-36(42(57)49-38)52-44(59)33-13-12-32(22-34(33)45(52)60)50-19-17-30(18-20-50)47-41(56)27-5-8-29(9-6-27)46-40(55)26-3-1-25(2-4-26)23-51(31-10-11-31)43(58)28-7-14-35-37(21-28)61-24-39(54)48-35/h1-9,12-14,21-22,30-31,36H,10-11,15-20,23-24H2,(H,46,55)(H,47,56)(H,48,54)(H,49,53,57)",
  "inchikey": "OHRABUZLZFHHEJ-UHFFFAOYSA-N",
  "isomeric_smiles": "C1CC1N(CC2=CC=C(C=C2)C(=O)NC3=CC=C(C=C3)C(=O)NC4CCN(CC4)C5=CC6=C(C=C5)C(=O)N(C6=O)C7CCC(=O)NC7=O)C(=O)C8=CC9=C(C=C8)NC(=O)CO9",
  "molecular_formula": "C45H41N7O9",
  "molecular_weight": "823.8",
  "name": "LLC0424",
  "primary_name": "LLC0424",
  "pubchem_cid": "171663346",
  "retrieval_date": "2026-10-26",
  "smiles": "C1CC1N(CC2=CC=C(C=C2)C(=O)NC3=CC=C(C=C3)C(=O)NC4CCN(CC4)C5=CC6=C(C=C5)C(=O)N(C6=O)C7CCC(=O)NC7=O)C(=O)C8=CC9=C(C=C8)NC(=O)CO9",
  "source_url": "https://pubchem.ncbi.nlm.nih.gov/compound/171663346",
  "source_urls": [
    "https://pubchem.ncbi.nlm.nih.gov/compound/171663346"
  ],
  "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
LLC0424PREP:LLC0424 NSD2 · protein-level evidence
Construct not curatedHomo sapiens		 DC50Immunoblot degradationcellular protein degradation = 20 nM0.02 µM · exact unit conversion
Experimental context
Replicates
Not curated
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
°C
Buffer
Not curated
Conditions
{'cell_line': 'RPMI-8402', 'readout': 'NSD2 protein'}
Qualification
Cellular whole-protein measurement. PWWP1-directed design is supported by the source, but no direct affinity is inferred and this result is not assigned to a PWWP domain.
 PMID:38687638 · 2024NCBI BioC full text; abstract, Results, chemical synthesis names and figure captions inspected
Original observation record
{
  "assay_construct_end": null,
  "assay_construct_start": null,
  "assay_context": "cellular_full_protein",
  "assay_organism": "Homo sapiens",
  "assay_record_id": "PWWP5:ASSAY:0025",
  "assay_type": "Immunoblot degradation",
  "assay_value_transferred_to_modeled_stereoisomers": false,
  "ccd_id": null,
  "chemical_id": "INCHIKEY:OHRABUZLZFHHEJ-UHFFFAOYSA-N",
  "compound_name": "LLC0424",
  "conditions": {
    "cell_line": "RPMI-8402",
    "readout": "NSD2 protein"
  },
  "domain": null,
  "domain_id": null,
  "endpoint": "DC50",
  "evidence_class": "cellular_protein_degradation",
  "evidence_location": "Abstract and Results",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11094793/",
  "gene": "NSD2",
  "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,
  "pdb_id": null,
  "preparation_id": "PREP:LLC0424",
  "protein_id": "UP:O96028",
  "publication_year": 2024,
  "reference_id": "PMID:38687638",
  "related_domain_id": "UP:O96028:PWWP1",
  "remaining_uncertainty": "Cellular whole-protein measurement. PWWP1-directed design is supported by the source, but no direct affinity is inferred and this result is not assigned to a PWWP domain.",
  "replicates": null,
  "retrieval_date": "2026-10-26",
  "role": "reported_degrader",
  "source_id": "P5:S:LIU2024",
  "source_reported_uncertainty": null,
  "source_reported_units": "nM",
  "source_reported_value": "20",
  "source_verification_scope": "NCBI BioC full text; abstract, Results, chemical synthesis names and figure captions inspected",
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "units": "nM",
  "value": 20,
  "value_operator": "=",
  "value_uM": 0.02,
  "verification_level": "primary_source_verified",
  "version": "phase5.chemical_curation.1.1.0"
}
LLC0424PREP:LLC0424 NSD2 · protein-level evidence
Construct not curatedHomo sapiens		 DmaxImmunoblot degradationcellular protein degradation = 96 percent
Experimental context
Replicates
Not curated
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
°C
Buffer
Not curated
Conditions
{'cell_line': 'RPMI-8402', 'readout': 'NSD2 protein'}
Qualification
Cellular whole-protein measurement. No PWWP-domain affinity inferred; replicate/uncertainty/duration not populated without assay-specific verification.
 PMID:38687638 · 2024NCBI BioC full text; abstract, Results, chemical synthesis names and figure captions inspected
Original observation record
{
  "assay_construct_end": null,
  "assay_construct_start": null,
  "assay_context": "cellular_full_protein",
  "assay_organism": "Homo sapiens",
  "assay_record_id": "PWWP5:ASSAY:0026",
  "assay_type": "Immunoblot degradation",
  "assay_value_transferred_to_modeled_stereoisomers": false,
  "ccd_id": null,
  "chemical_id": "INCHIKEY:OHRABUZLZFHHEJ-UHFFFAOYSA-N",
  "compound_name": "LLC0424",
  "conditions": {
    "cell_line": "RPMI-8402",
    "readout": "NSD2 protein"
  },
  "domain": null,
  "domain_id": null,
  "endpoint": "Dmax",
  "evidence_class": "cellular_protein_degradation",
  "evidence_location": "Abstract and Results",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11094793/",
  "gene": "NSD2",
  "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,
  "pdb_id": null,
  "preparation_id": "PREP:LLC0424",
  "protein_id": "UP:O96028",
  "publication_year": 2024,
  "reference_id": "PMID:38687638",
  "related_domain_id": "UP:O96028:PWWP1",
  "remaining_uncertainty": "Cellular whole-protein measurement. No PWWP-domain affinity inferred; replicate/uncertainty/duration not populated without assay-specific verification.",
  "replicates": null,
  "retrieval_date": "2026-10-26",
  "role": "reported_degrader",
  "source_id": "P5:S:LIU2024",
  "source_reported_uncertainty": null,
  "source_reported_units": "percent",
  "source_reported_value": "96",
  "source_verification_scope": "NCBI BioC full text; abstract, Results, chemical synthesis names and figure captions inspected",
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "units": "percent",
  "value": 96,
  "value_operator": "=",
  "value_uM": null,
  "verification_level": "primary_source_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

LLC0424

PREP:LLC0424

Neutral parent/reference identity shown separately from the experimentally assayed preparation; salt, solvent and lot composition not independently established. PubChem structure has unspecified stereochemistry, which is preserved rather than assigned.

reported degrader
Complete preparation record
{
  "aliases": [
    "compound 10l (Liu 2024)"
  ],
  "chemical_id": "INCHIKEY:OHRABUZLZFHHEJ-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. PubChem structure has unspecified stereochemistry, which is preserved rather than assigned.",
  "identity_status": "resolved_reference_parent_preparation_form_unresolved",
  "molecular_entity_type": "small_molecule_preparation",
  "name": "LLC0424",
  "phase5_identity_overlay": false,
  "preparation_id": "PREP:LLC0424",
  "retrieval_date": "2026-10-26",
  "role": "reported_degrader",
  "source_id": "P5:S:LIU2024",
  "source_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11094793/",
  "version": "phase5.chemical_curation.1.1.0"
}

Provenance and reproducibility

Sources & downloads

https://pmc.ncbi.nlm.nih.gov/articles/PMC11094793/https://pubchem.ncbi.nlm.nih.gov/compound/171663346
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.