Experimental preparationIdentity not assigned

Measurements remain attached to the reported preparation.

Reported experimental preparation

compound 11 (Collie 2025)

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

Assayed diastereomeric preparation: pyrrolidine 2S fixed and sulfolane center racemic in the SI name. A1IEG/A1IFS are modeled candidates in 9FOC; mixture affinity is not assigned to either pure stereoisomer. Composition ratio and fraction-to-CCD assignment remain unresolved.

NSD2 PWWP1 NSD3 PWWP1

3 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.

Preparation	Tested target & construct	Method / endpoint	Original observation	Conditions & uncertainty	Source & verification
compound 11 (Collie 2025)PREP:COLLIE2025_11	NSD2 PWWP1 208–368Homo sapiens	KdSPR Kddirect binding affinity	= 1.02 ± 0.19 µM1.02 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:0018", "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:0018\", \"assay_type\": \"SPR Kd\", \"ccd_id\": null, \"compound_name\": \"compound 11 (Collie 2025)\", \"conditions\": {\"protein_construct\": \"NSD2 208\u2013368\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}, \"crystallographic_component_ids\": [\"A1IFS\", \"A1IEG\"], \"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. Compound 11 is the assayed preparation; 9FOC models two stereoisomer CCDs. Do not assign the aggregate affinity separately to each pure stereoisomer.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"9FOC\", \"reference_id\": \"PMID:40959233\", \"role\": \"experimentally_studied_ligand\", \"uncertainty\": 0.19, \"units\": \"\u00b5M\", \"value\": 1.02, \"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": "assayed_stereoisomeric_mixture_not_single_chemical_identity", "component_context": null, "compound_name": "compound 11 (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": "[\"A1IFS\", \"A1IEG\"]", "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. Compound 11 is the assayed preparation; 9FOC models two stereoisomer CCDs. Do not assign the aggregate affinity separately to each pure stereoisomer.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": "9FOC", "preparation_id": "PREP:COLLIE2025_11", "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": "0.19", "source_reported_units": "\u00b5M", "source_reported_value": "1.02", "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": 1.02, "value_operator": "=", "value_uM": 1.02, "verification_level": "primary_full_text_sections_verified" }
compound 11 (Collie 2025)PREP:COLLIE2025_11	NSD2 PWWP1 211–350Homo sapiens	KdSPR Kddirect binding affinity	= 2.3 ± 0.31 µM2.3 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:0025", "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:0025\", \"assay_type\": \"SPR Kd\", \"ccd_id\": null, \"compound_name\": \"compound 11 (Collie 2025)\", \"conditions\": {\"protein_construct\": \"NSD2 211\u2013350\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}, \"crystallographic_component_ids\": [\"A1IFS\", \"A1IEG\"], \"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. Compound 11 is the assayed preparation; 9FOC models two stereoisomer CCDs. Do not assign the aggregate affinity separately to each pure stereoisomer.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"9FOC\", \"reference_id\": \"PMID:40959233\", \"role\": \"experimentally_studied_ligand\", \"uncertainty\": 0.31, \"units\": \"\u00b5M\", \"value\": 2.3, \"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": "assayed_stereoisomeric_mixture_not_single_chemical_identity", "component_context": null, "compound_name": "compound 11 (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": "[\"A1IFS\", \"A1IEG\"]", "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. Compound 11 is the assayed preparation; 9FOC models two stereoisomer CCDs. Do not assign the aggregate affinity separately to each pure stereoisomer.", "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": 7.5, "pdb_id": "9FOC", "preparation_id": "PREP:COLLIE2025_11", "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": "0.31", "source_reported_units": "\u00b5M", "source_reported_value": "2.3", "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": 0.31, "uncertainty_type": "SD", "uncertainty_uM": 0.31, "unit_conversion": null, "units": "\u00b5M", "value": 2.3, "value_operator": "=", "value_uM": 2.3, "verification_level": "primary_full_text_sections_verified" }
compound 11 (Collie 2025)PREP:COLLIE2025_11Negative / censored	NSD3 PWWP1 263–398Homo sapiens	KdSPR Kd counter-screennegative binding test	No binding	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:0005", "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": "assayed_stereoisomeric_mixture_not_single_chemical_identity", "component_context": null, "compound_name": "compound 11 (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": "negative_binding_test", "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_11", "protein_id": "UP:Q9BZ95", "qualitative_result": "No binding", "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": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": null }

Preparation

Tested target & construct

Method / endpoint

Original observation

Conditions & uncertainty

Source & verification

compound 11 (Collie 2025)PREP:COLLIE2025_11

NSD2 PWWP1
208–368Homo sapiens

KdSPR Kddirect binding affinity

= 1.02 ± 0.19 µM1.02 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:0018",
  "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:0018\", \"assay_type\": \"SPR Kd\", \"ccd_id\": null, \"compound_name\": \"compound 11 (Collie 2025)\", \"conditions\": {\"protein_construct\": \"NSD2 208\u2013368\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}, \"crystallographic_component_ids\": [\"A1IFS\", \"A1IEG\"], \"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. Compound 11 is the assayed preparation; 9FOC models two stereoisomer CCDs. Do not assign the aggregate affinity separately to each pure stereoisomer.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"9FOC\", \"reference_id\": \"PMID:40959233\", \"role\": \"experimentally_studied_ligand\", \"uncertainty\": 0.19, \"units\": \"\u00b5M\", \"value\": 1.02, \"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": "assayed_stereoisomeric_mixture_not_single_chemical_identity",
  "component_context": null,
  "compound_name": "compound 11 (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": "[\"A1IFS\", \"A1IEG\"]",
  "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. Compound 11 is the assayed preparation; 9FOC models two stereoisomer CCDs. Do not assign the aggregate affinity separately to each pure stereoisomer.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_report",
  "numeric_value_inferred_from_structure": 0,
  "pH": 7.5,
  "pdb_id": "9FOC",
  "preparation_id": "PREP:COLLIE2025_11",
  "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": "0.19",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "1.02",
  "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": 1.02,
  "value_operator": "=",
  "value_uM": 1.02,
  "verification_level": "primary_full_text_sections_verified"
}

compound 11 (Collie 2025)PREP:COLLIE2025_11

NSD2 PWWP1
211–350Homo sapiens

KdSPR Kddirect binding affinity

= 2.3 ± 0.31 µM2.3 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:0025",
  "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:0025\", \"assay_type\": \"SPR Kd\", \"ccd_id\": null, \"compound_name\": \"compound 11 (Collie 2025)\", \"conditions\": {\"protein_construct\": \"NSD2 211\u2013350\", \"replicates\": \"at least 3\", \"uncertainty_type\": \"SD\"}, \"crystallographic_component_ids\": [\"A1IFS\", \"A1IEG\"], \"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. Compound 11 is the assayed preparation; 9FOC models two stereoisomer CCDs. Do not assign the aggregate affinity separately to each pure stereoisomer.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"9FOC\", \"reference_id\": \"PMID:40959233\", \"role\": \"experimentally_studied_ligand\", \"uncertainty\": 0.31, \"units\": \"\u00b5M\", \"value\": 2.3, \"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": "assayed_stereoisomeric_mixture_not_single_chemical_identity",
  "component_context": null,
  "compound_name": "compound 11 (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": "[\"A1IFS\", \"A1IEG\"]",
  "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. Compound 11 is the assayed preparation; 9FOC models two stereoisomer CCDs. Do not assign the aggregate affinity separately to each pure stereoisomer.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_report",
  "numeric_value_inferred_from_structure": 0,
  "pH": 7.5,
  "pdb_id": "9FOC",
  "preparation_id": "PREP:COLLIE2025_11",
  "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": "0.31",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "2.3",
  "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": 0.31,
  "uncertainty_type": "SD",
  "uncertainty_uM": 0.31,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 2.3,
  "value_operator": "=",
  "value_uM": 2.3,
  "verification_level": "primary_full_text_sections_verified"
}

compound 11 (Collie 2025)PREP:COLLIE2025_11Negative / censored

NSD3 PWWP1
263–398Homo sapiens

KdSPR Kd counter-screennegative binding test

No binding

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:0005",
  "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": "assayed_stereoisomeric_mixture_not_single_chemical_identity",
  "component_context": null,
  "compound_name": "compound 11 (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": "negative_binding_test",
  "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_11",
  "protein_id": "UP:Q9BZ95",
  "qualitative_result": "No binding",
  "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": null,
  "value": null,
  "value_operator": null,
  "value_uM": null,
  "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.

Source-associated entries, without an exact identity/instance match: 9FOC

Preparations, identities and controls remain separate

Experimental context

compound 11 (Collie 2025)

PREP:COLLIE2025_11

assay preparation

Complete preparation record

{
  "chemical_id": null,
  "entity_type": "small_molecule_preparation",
  "exact_ccd_id": null,
  "identity_note": "Assayed diastereomeric preparation: pyrrolidine 2S fixed and sulfolane center racemic in the SI name. A1IEG/A1IFS are modeled candidates in 9FOC; mixture affinity is not assigned to either pure stereoisomer. Composition ratio and fraction-to-CCD assignment remain unresolved.",
  "identity_status": "assayed_stereoisomeric_mixture_not_single_chemical_identity",
  "modeled_candidate_ccd_ids": "[\"A1IEG\", \"A1IFS\"]",
  "modeled_candidate_chemical_ids": "[\"INCHIKEY:FPDVOQXTUVFQHW-KBPBESRZSA-N\", \"INCHIKEY:FPDVOQXTUVFQHW-KGLIPLIRSA-N\"]",
  "name": "compound 11 (Collie 2025)",
  "preparation_id": "PREP:COLLIE2025_11",
  "role": "assay_preparation",
  "sequence_if_defined": null
}

Source-supported relationships

Relationship	Related identity / preparation	Scope	Source
modeled candidate not exact identity	(2S)-1-[4-[[(3S)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide	Assayed diastereomeric preparation: pyrrolidine 2S fixed and sulfolane center racemic in the SI name. A1IEG/A1IFS are modeled candidates in 9FOC; mixture affinity is not assigned to either pure stereoisomer. Composition ratio and fraction-to-CCD assignment remain unresolved.	Source
modeled candidate not exact identity	(2S)-1-[4-[[(3R)-1,1-bis(oxidanylidene)thiolan-3-yl]methyl-methyl-amino]-6-methyl-pyrimidin-2-yl]-N-methyl-pyrrolidine-2-carboxamide	Assayed diastereomeric preparation: pyrrolidine 2S fixed and sulfolane center racemic in the SI name. A1IEG/A1IFS are modeled candidates in 9FOC; mixture affinity is not assigned to either pure stereoisomer. Composition ratio and fraction-to-CCD assignment remain unresolved.	Source

Provenance and reproducibility

Sources & downloads

https://pmc.ncbi.nlm.nih.gov/articles/PMC12434523/

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.