Resolved chemical identity

UNC6934

Studied + deposited research ligandReported chemical probeNegative / censored observations

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

6 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:KOZGEDUWAQFVAV-UHFFFAOYSA-N
Full InChIKey: KOZGEDUWAQFVAV-UHFFFAOYSA-N
Source identity status: complete deposited InChIKey
Deposited CCD identifiers: V01
External identifiers: See deposited identity and source links

Reference formula: C24H21N5O4
Calculated molecular weight: 443.463
Calculated descriptors: cLogP 2.8646 · TPSA 113.52 Å² · HBD 2 · HBA 6RDKit 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: c1cc(ccc1CN(C2CC2)C(=O)c3ccc4c(c3)OCC(=O)N4)C(=O)Nc5ccncn5
InChI: Not curated

{
  "aliases": [
    "N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide"
  ],
  "ccd_ids": [
    "V01"
  ],
  "ccd_names": "[\"N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide\"]",
  "ccd_types": "[\"non-polymer\"]",
  "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N",
  "connectivity_block": "KOZGEDUWAQFVAV",
  "curated_source_sha256": null,
  "curation_version": "frozen-v1.2",
  "external_identifiers": {},
  "formal_charge_by_ccd": "{\"V01\": 0}",
  "formulae": "[\"C24 H21 N5 O4\"]",
  "geometry_note": "CCD ideal SDF is a reference chemical geometry, not a deposited bound pose.",
  "identity_status": "complete_deposited_InChIKey",
  "inchikey": "KOZGEDUWAQFVAV-UHFFFAOYSA-N",
  "inventory_origin": "v1_CCD_inventory",
  "isomeric_smiles": "c1cc(ccc1CN(C2CC2)C(=O)c3ccc4c(c3)OCC(=O)N4)C(=O)Nc5ccncn5",
  "primary_name": "N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide",
  "retrieval_date": "2026-10-24",
  "smiles_stereo_by_ccd": "{\"V01\": \"c1cc(ccc1CN(C2CC2)C(=O)c3ccc4c(c3)OCC(=O)N4)C(=O)Nc5ccncn5\"}",
  "source_metadata_sha256": "{\"V01\": \"ced5ef4acd208273eb85fecdbbc375b05202a622e993dc4571d4354dcab003ca\"}",
  "source_urls": [
    "https://www.rcsb.org/ligand/V01"
  ]
}

Source aliases (2)

N-cyclopropyl-3-oxo-N-({4-[(pyrimidin-4-yl)carbamoyl]phenyl}methyl)-3,4-dihydro-2H-1,4-benzoxazine-7-carboxamide
UNC6934

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
UNC6934PREP:UNC6934	NSD2 PWWP1 208–368Homo sapiens	KdSPR Kddirect binding affinity	= 91 ± 8 nM0.091 µM · exact unit conversion	Experimental context Replicates 3 (triplicate experiments; independence level not specified) Uncertainty definition Not curated; do not assume SD or SEM Temperature — Buffer 10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.05% Tween-20; 0.5% DMSO Conditions {"phase3_verification": "SV02A", "protein_construct": "NSD2 208–368", "purified_tags": "AviTag/NSD2(208–368)/polyhistidine; biotinylated", "source_protocol_highest_concentration_uM": 2} Qualification SPR temperature and exact uncertainty definition are not specified in the inspected assay-specific source. Triplicate experiments reported. Preparation/assay construct differs from crystallization 211–350.	PMID:34782742 · 2022Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained Original observation record { "DMSO_percent": 0.5, "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:0004", "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:0004\", \"assay_type\": \"SPR Kd\", \"ccd_id\": \"V01\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"UNC6934\", \"conditions\": {\"protein_construct\": \"NSD2 208\u2013368\"}, \"domain\": \"PWWP1\", \"evidence_location\": \"Results; Figures 1\u20132\", \"evidence_url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/\", \"gene\": \"NSD2\", \"interpretation\": \"\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"6XCG\", \"reference_id\": \"PMID:34782742\", \"role\": \"reported_chemical_probe\", \"uncertainty\": 8, \"units\": \"nM\", \"value\": 91, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}", "buffer": "10 mM HEPES; 150 mM NaCl; 3 mM EDTA; 0.05% Tween-20; 0.5% DMSO", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208\u2013368\", \"purified_tags\": \"AviTag/NSD2(208\u2013368)/polyhistidine; biotinylated\", \"source_protocol_highest_concentration_uM\": 2}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results; Figures 1\u20132", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.4, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "SPR temperature and exact uncertainty definition are not specified in the inspected assay-specific source. Triplicate experiments reported. Preparation/assay construct differs from crystallization 211\u2013350.", "replicates": "3 (triplicate experiments; independence level not specified)", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "8", "source_reported_units": "nM", "source_reported_value": "91", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": null, "uncertainty": 8.0, "uncertainty_type": null, "uncertainty_uM": 0.008, "unit_conversion": null, "units": "nM", "value": 91.0, "value_operator": "=", "value_uM": 0.091, "verification_level": "primary_full_text_sections_verified" }
UNC6934PREP:UNC6934	NSD2 PWWP1 208–368Homo sapiens	IC50AlphaScreen IC50biochemical interaction inhibition	= 104 ± 13 nM0.104 µM · exact unit conversion	Experimental context Replicates 3 independent experiments; each 10-point curve in duplicate Uncertainty definition Not curated; do not assume SD or SEM Temperature 23 °C Buffer 150 mM NaCl; 20 mM Tris; 0.01% BSA; 0.01% NP-40; 1 mM DTT (DTT omitted from bead buffer) Conditions {"phase3_verification": "SV02A", "protein_construct": "NSD2 208–368", "readout": "His-NSD2-PWWP1 binding to H3K36me2 designer nucleosome", "tag": "6His", "temperature_scope": "23°C compound/protein and nucleosome preincubation; bead incubation room temperature"} Qualification 23°C is the antagonist preincubation temperature, not a verified readout temperature. Final DMSO fraction and SD-versus-SEM definition for ±13 nM are not explicit in the inspected assay-specific text.	PMID:34782742 · 2022Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained 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:0005", "assay_type": "AlphaScreen 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:0005\", \"assay_type\": \"AlphaScreen IC50\", \"ccd_id\": \"V01\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"UNC6934\", \"conditions\": {}, \"domain\": \"PWWP1\", \"evidence_location\": \"Discussion; biochemical characterization\", \"evidence_url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/\", \"gene\": \"NSD2\", \"interpretation\": \"Binding-interaction assay, not a direct catalytic SET-domain inhibition measurement.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"6XCG\", \"reference_id\": \"PMID:34782742\", \"role\": \"reported_chemical_probe\", \"uncertainty\": 13, \"units\": \"nM\", \"value\": 104, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}", "buffer": "150 mM NaCl; 20 mM Tris; 0.01% BSA; 0.01% NP-40; 1 mM DTT (DTT omitted from bead buffer)", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"phase3_verification\": \"SV02A\", \"protein_construct\": \"NSD2 208\u2013368\", \"readout\": \"His-NSD2-PWWP1 binding to H3K36me2 designer nucleosome\", \"tag\": \"6His\", \"temperature_scope\": \"23\u00b0C compound/protein and nucleosome preincubation; bead incubation room temperature\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "biochemical_interaction_inhibition", "evidence_location": "Discussion; biochemical characterization", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": "Binding-interaction assay, not a direct catalytic SET-domain inhibition measurement.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "23\u00b0C is the antagonist preincubation temperature, not a verified readout temperature. Final DMSO fraction and SD-versus-SEM definition for \u00b113 nM are not explicit in the inspected assay-specific text.", "replicates": "3 independent experiments; each 10-point curve in duplicate", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "13", "source_reported_units": "nM", "source_reported_value": "104", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": 23, "uncertainty": 13.0, "uncertainty_type": null, "uncertainty_uM": 0.013, "unit_conversion": null, "units": "nM", "value": 104.0, "value_operator": "=", "value_uM": 0.104, "verification_level": "primary_full_text_sections_verified" }
UNC6934PREP:UNC6934	NSD2 PWWP1 Construct not curatedHomo sapiens	Unstandardized half-response concentrationNanoBRET PPI half-responsecellular interaction response	= 1.23 ± 0.25 µM	Experimental context Replicates 3 independent replicates Uncertainty definition Not curated; do not assume SD or SEM Temperature — Buffer DMEM/F12 without phenol red; 4% FBS; 100 U/mL penicillin; 100 ug/mL streptomycin Conditions {"cell_line": "U2OS", "readout": "NSD2 PWWP1–histone H3.3 interaction"} Qualification NanoLuc construct boundaries, readout temperature and SD-versus-SEM are not explicit in the inspected source. Results say EC50 while Discussion says IC50; neutral half-response label retained.	PMID:34782742 · 2022Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained 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:0006", "assay_type": "NanoBRET PPI half-response", "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:0006\", \"assay_type\": \"NanoBRET PPI half-response\", \"ccd_id\": \"V01\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"UNC6934\", \"conditions\": {\"cell_line\": \"U2OS\", \"readout\": \"NSD2 PWWP1\u2013histone H3.3 interaction\"}, \"domain\": \"PWWP1\", \"evidence_location\": \"Results: cellular target engagement; Figure 4d\", \"evidence_url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/\", \"gene\": \"NSD2\", \"interpretation\": \"Main Results calls this EC50; Discussion calls it IC50. Original value retained without conflating it with Kd.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"6XCG\", \"reference_id\": \"PMID:34782742\", \"role\": \"reported_chemical_probe\", \"uncertainty\": 0.25, \"units\": \"\u00b5M\", \"value\": 1.23, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}", "buffer": "DMEM/F12 without phenol red; 4% FBS; 100 U/mL penicillin; 100 ug/mL streptomycin", "ccd_id": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "UNC6934", "conditions": "{\"cell_line\": \"U2OS\", \"readout\": \"NSD2 PWWP1\u2013histone H3.3 interaction\"}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": "Results/Figure use EC50, Discussion uses IC50; neutral half-response retained", "evidence_class": "cellular_interaction_response", "evidence_location": "Results: cellular target engagement; Figure 4d", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": "Main Results calls this EC50; Discussion calls it IC50. Original value retained without conflating it with Kd.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": null, "pdb_id": "6XCG", "preparation_id": "PREP:UNC6934", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "NanoLuc construct boundaries, readout temperature and SD-versus-SEM are not explicit in the inspected source. Results say EC50 while Discussion says IC50; neutral half-response label retained.", "replicates": "3 independent replicates", "role": "reported_chemical_probe", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "0.25", "source_reported_units": "\u00b5M", "source_reported_value": "1.23", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": null, "uncertainty": 0.25, "uncertainty_type": null, "uncertainty_uM": 0.25, "unit_conversion": null, "units": "\u00b5M", "value": 1.23, "value_operator": "=", "value_uM": 1.23, "verification_level": "primary_full_text_sections_verified" }
UNC6934PREP:UNC6934	NSD2 PWWP1 208–368Homo sapiens	KdSPR Kddirect binding affinity	= 0.24 ± 0.03 µM0.24 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:0014", "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:0014\", \"assay_type\": \"SPR Kd\", \"ccd_id\": \"V01\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"UNC6934\", \"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\": \"reported_chemical_probe\", \"uncertainty\": 0.03, \"units\": \"\u00b5M\", \"value\": 0.24, \"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": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "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\": \"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:UNC6934", "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": "reported_chemical_probe", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.03", "source_reported_units": "\u00b5M", "source_reported_value": "0.24", "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": 0.03, "uncertainty_type": "SD", "uncertainty_uM": 0.03, "unit_conversion": null, "units": "\u00b5M", "value": 0.24, "value_operator": "=", "value_uM": 0.24, "verification_level": "primary_full_text_sections_verified" }
UNC6934PREP:UNC6934	NSD2 PWWP1 211–350Homo sapiens	KdSPR Kddirect binding affinity	= 1.33 ± 0.19 µM1.33 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:0021", "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:0021\", \"assay_type\": \"SPR Kd\", \"ccd_id\": \"V01\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"UNC6934\", \"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\": \"reported_chemical_probe\", \"uncertainty\": 0.19, \"units\": \"\u00b5M\", \"value\": 1.33, \"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": "V01", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "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\": \"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:UNC6934", "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": "reported_chemical_probe", "source_component_url": null, "source_id": "S05", "source_reported_uncertainty": "0.19", "source_reported_units": "\u00b5M", "source_reported_value": "1.33", "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": 0.19, "uncertainty_type": "SD", "uncertainty_uM": 0.19, "unit_conversion": null, "units": "\u00b5M", "value": 1.33, "value_operator": "=", "value_uM": 1.33, "verification_level": "primary_full_text_sections_verified" }
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 }

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
6XCG · V01PDB:6XCG:LIG:D:V01:401:.	NSD2 PWWP1Protein label chain A · ligand label chain D	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.8613 Å Pfam: 2.8613 Å	View deposited instance
6XCG · V01PDB:6XCG:LIG:E:V01:401:.	NSD2 PWWP1Protein label chain B · ligand label chain E	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9125 Å Pfam: 2.8758 Å	View deposited instance
6XCG · V01PDB:6XCG:LIG:I:V01:401:.	NSD2 PWWP1Protein label chain C · ligand label chain I	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.886 Å Pfam: 2.794 Å	View deposited instance

Preparations, identities and controls remain separate

Experimental context

UNC6934

PREP:UNC6934

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

assay preparation

Complete preparation record

{
  "chemical_id": "INCHIKEY:KOZGEDUWAQFVAV-UHFFFAOYSA-N",
  "entity_type": "small_molecule_preparation",
  "exact_ccd_id": "V01",
  "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": "UNC6934",
  "preparation_id": "PREP:UNC6934",
  "role": "assay_preparation",
  "sequence_if_defined": null
}

Source-supported relationships

Relationship	Related identity / preparation	Scope	Source
has negative control for	UNC7145	NSD2-PWWP1 probe negative control	Source

Provenance and reproducibility

Sources & downloads

https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/https://www.rcsb.org/ligand/V01

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.