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

Resolved chemical identity

BPP

Studied + deposited research ligandNegative / censored observations

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

PSIP1 PWWP1BRPF1 PWWP1GLYR1 PWWP1HDGFL2 PWWP1DNMT3B PWWP1HDGFL3 PWWP1
8 assay / association records1 preparations2 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:LKKNQJJSEMQTHQ-UHFFFAOYSA-N
Full InChIKey
LKKNQJJSEMQTHQ-UHFFFAOYSA-N
Source identity status
complete deposited InChIKey
Deposited CCD identifiers
A1D73
External identifiers
See deposited identity and source links
Reference formula
C8H6BrN3
Calculated molecular weight
224.061
Calculated descriptors
cLogP 2.2342 · TPSA 41.57 Ų · HBD 1 · HBA 2RDKit 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
c1cnccc1c2c(c[nH]n2)Br
InChI
Not curated
{
  "aliases": [
    "4-(4-bromanyl-1~{H}-pyrazol-3-yl)pyridine"
  ],
  "ccd_ids": [
    "A1D73"
  ],
  "ccd_names": "[\"4-(4-bromanyl-1~{H}-pyrazol-3-yl)pyridine\"]",
  "ccd_types": "[\"non-polymer\"]",
  "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "connectivity_block": "LKKNQJJSEMQTHQ",
  "curated_source_sha256": null,
  "curation_version": "frozen-v1.2",
  "external_identifiers": {},
  "formal_charge_by_ccd": "{\"A1D73\": 0}",
  "formulae": "[\"C8 H6 Br N3\"]",
  "geometry_note": "CCD ideal SDF is a reference chemical geometry, not a deposited bound pose.",
  "identity_status": "complete_deposited_InChIKey",
  "inchikey": "LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "inventory_origin": "v1_CCD_inventory",
  "isomeric_smiles": "c1cnccc1c2c(c[nH]n2)Br",
  "primary_name": "4-(4-bromanyl-1~{H}-pyrazol-3-yl)pyridine",
  "retrieval_date": "2026-10-24",
  "smiles_stereo_by_ccd": "{\"A1D73\": \"c1cnccc1c2c(c[nH]n2)Br\"}",
  "source_metadata_sha256": "{\"A1D73\": \"0a1b5e70da9485a8ac9dec8cef8886ee561ff0416a4e42562c12bf063bee65ec\"}",
  "source_urls": [
    "https://www.rcsb.org/ligand/A1D73"
  ]
}
Source aliases (2)
  • 4-(4-bromanyl-1~{H}-pyrazol-3-yl)pyridine
  • BPP

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
BPPPREP:BPP HDGFL2 PWWP
1–93Homo sapiens		 KdNMR chemical-shift perturbation Kddirect binding affinity = 7 ± 5 µM7 µM · exact unit conversion
Experimental context
Replicates
Not curated
Uncertainty definition
fitting_error
Temperature
—
Buffer
HEPES-buffered saline; exact buffer/salt concentrations not restated in CSP subsection
Conditions
{"fit_model": "1:1 binding; global fit with shared Kd", "ligand_to_protein_molar_ratio_range": [0, 6], "protein_concentration_uM": 100, "protein_construct": "HDGFL2 1–93"}
Qualification
Intermediate-exchange NMR fit has large fitting error; ITC cross-validation reported, exact separate ITC number not extracted.
 PMID:39031937 · 2024primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved
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": 93,
  "assay_construct_start": 1,
  "assay_record_id": "PWWP:ASSAY:0011",
  "assay_type": "NMR chemical-shift perturbation 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:0011\", \"assay_type\": \"NMR chemical-shift perturbation Kd\", \"ccd_id\": \"A1D73\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"BPP\", \"conditions\": {}, \"domain\": \"PWWP\", \"evidence_location\": \"Results; Figure 1E\", \"evidence_url\": \"https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981\", \"gene\": \"HDGFL2\", \"interpretation\": \"Authors report intermediate-exchange limitations and additional ITC validation. This record preserves the NMR value and fitting error.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"8Z6C\", \"reference_id\": \"PMID:39031937\", \"role\": \"experimentally_studied_fragment_ligand\", \"uncertainty\": 5, \"units\": \"\u00b5M\", \"value\": 7, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}",
  "buffer": "HEPES-buffered saline; exact buffer/salt concentrations not restated in CSP subsection",
  "ccd_id": "A1D73",
  "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json",
  "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "chemical_identity_status": "exact_single_CCD_identity",
  "component_context": null,
  "compound_name": "BPP",
  "conditions": "{\"fit_model\": \"1:1 binding; global fit with shared Kd\", \"ligand_to_protein_molar_ratio_range\": [0, 6], \"protein_concentration_uM\": 100, \"protein_construct\": \"HDGFL2 1\u201393\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP",
  "domain_id": "UP:Q7Z4V5:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Results; Figure 1E",
  "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981",
  "gene": "HDGFL2",
  "interpretation": "Authors report intermediate-exchange limitations and additional ITC validation. This record preserves the NMR value and fitting error.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_report",
  "numeric_value_inferred_from_structure": 0,
  "pH": 7.4,
  "pdb_id": "8Z6C",
  "preparation_id": "PREP:BPP",
  "protein_id": "UP:Q7Z4V5",
  "qualitative_result": null,
  "reference_id": "PMID:39031937",
  "remaining_uncertainty": "Intermediate-exchange NMR fit has large fitting error; ITC cross-validation reported, exact separate ITC number not extracted.",
  "replicates": null,
  "role": "experimentally_studied_fragment_ligand",
  "source_component_url": null,
  "source_id": "S04",
  "source_reported_uncertainty": "5",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "7",
  "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved",
  "temperature_C": null,
  "uncertainty": 5.0,
  "uncertainty_type": "fitting_error",
  "uncertainty_uM": 5.0,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 7.0,
  "value_operator": "=",
  "value_uM": 7.0,
  "verification_level": "primary_full_text_sections_verified"
}
BPPPREP:BPP PSIP1 PWWP
Construct not curatedHomo sapiens		 KdITC Kddirect binding affinity = 27 ± 2 µM27 µM · exact unit conversion
Experimental context
Replicates
Not curated
Uncertainty definition
fitting_error
Temperature
—
Buffer
Not curated
Conditions
{}
Qualification
Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.
 PMID:39031937 · 2024primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved
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:0012",
  "assay_type": "ITC 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:0012\", \"assay_type\": \"ITC Kd\", \"ccd_id\": \"A1D73\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"BPP\", \"conditions\": {}, \"domain\": \"PWWP\", \"evidence_location\": \"Results; Figure 4B\", \"evidence_url\": \"https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981\", \"gene\": \"PSIP1\", \"interpretation\": \"Binding is established in solution; no PSIP1\u2013BPP crystal structure is assigned here.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": null, \"reference_id\": \"PMID:39031937\", \"role\": \"experimentally_studied_fragment_ligand\", \"uncertainty\": 2, \"units\": \"\u00b5M\", \"value\": 27, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}",
  "buffer": null,
  "ccd_id": "A1D73",
  "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json",
  "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "chemical_identity_status": "exact_single_CCD_identity",
  "component_context": null,
  "compound_name": "BPP",
  "conditions": "{}",
  "crystallographic_component_ids": null,
  "domain": "PWWP",
  "domain_id": "UP:O75475:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Results; Figure 4B",
  "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981",
  "gene": "PSIP1",
  "interpretation": "Binding is established in solution; no PSIP1\u2013BPP crystal structure is assigned here.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_report",
  "numeric_value_inferred_from_structure": 0,
  "pH": null,
  "pdb_id": null,
  "preparation_id": "PREP:BPP",
  "protein_id": "UP:O75475",
  "qualitative_result": null,
  "reference_id": "PMID:39031937",
  "remaining_uncertainty": "Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent.",
  "replicates": null,
  "role": "experimentally_studied_fragment_ligand",
  "source_component_url": null,
  "source_id": "S04",
  "source_reported_uncertainty": "2",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "27",
  "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved",
  "temperature_C": null,
  "uncertainty": 2.0,
  "uncertainty_type": "fitting_error",
  "uncertainty_uM": 2.0,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 27.0,
  "value_operator": "=",
  "value_uM": 27.0,
  "verification_level": "primary_full_text_sections_verified"
}
BPPPREP:BPP HDGFL3 PWWP
Construct not curatedHomo sapiens		 KdBinding Kd; specific assay in Figure S2 not independently inspecteddirect binding affinity = 14 ± 2 µM14 µM · exact unit conversion
Experimental context
Replicates
Not curated
Uncertainty definition
fitting_error
Temperature
—
Buffer
Not curated
Conditions
{}
Qualification
14 ± 2 µM confirmed in primary Results; specific Figure S2 assay method remains unresolved.
 PMID:39031937 · 2024primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved
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:0013",
  "assay_type": "Binding Kd; specific assay in Figure S2 not independently inspected",
  "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:0013\", \"assay_type\": \"Binding Kd; specific assay in Figure S2 not independently inspected\", \"ccd_id\": \"A1D73\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"BPP\", \"conditions\": {}, \"domain\": \"PWWP\", \"evidence_location\": \"Results: selectivity paragraph\", \"evidence_url\": \"https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981\", \"gene\": \"HDGFL3\", \"interpretation\": \"Numerical result verified in main text; precise supporting-assay details remain to be checked.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": null, \"reference_id\": \"PMID:39031937\", \"role\": \"experimentally_studied_fragment_ligand\", \"uncertainty\": 2, \"units\": \"\u00b5M\", \"value\": 14, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}",
  "buffer": null,
  "ccd_id": "A1D73",
  "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json",
  "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "chemical_identity_status": "exact_single_CCD_identity",
  "component_context": null,
  "compound_name": "BPP",
  "conditions": "{}",
  "crystallographic_component_ids": null,
  "domain": "PWWP",
  "domain_id": "UP:Q9Y3E1:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Results: selectivity paragraph",
  "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981",
  "gene": "HDGFL3",
  "interpretation": "Numerical result verified in main text; precise supporting-assay details remain to be checked.",
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_report",
  "numeric_value_inferred_from_structure": 0,
  "pH": null,
  "pdb_id": null,
  "preparation_id": "PREP:BPP",
  "protein_id": "UP:Q9Y3E1",
  "qualitative_result": null,
  "reference_id": "PMID:39031937",
  "remaining_uncertainty": "14 \u00b1 2 \u00b5M confirmed in primary Results; specific Figure S2 assay method remains unresolved.",
  "replicates": null,
  "role": "experimentally_studied_fragment_ligand",
  "source_component_url": null,
  "source_id": "S04",
  "source_reported_uncertainty": "2",
  "source_reported_units": "\u00b5M",
  "source_reported_value": "14",
  "source_verification_scope": "primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved",
  "temperature_C": null,
  "uncertainty": 2.0,
  "uncertainty_type": "fitting_error",
  "uncertainty_uM": 2.0,
  "unit_conversion": null,
  "units": "\u00b5M",
  "value": 14.0,
  "value_operator": "=",
  "value_uM": 14.0,
  "verification_level": "primary_full_text_sections_verified"
}
BPPPREP:BPP HDGFL2 PWWP1
1–93Variant: Y18SHomo sapiens		 KdNMR chemical-shift perturbation Kddirect binding affinity = 0.29 ± 0.02 mM290 µM · exact unit conversion
Experimental context
Replicates
Not curated
Uncertainty definition
fitting error
Temperature
°C
Buffer
Not curated
Conditions
{'binding_model': '1:1 global fit of perturbed residues', 'buffer': 'HEPES-buffered saline; CSP subsection does not separately give HEPES/NaCl concentrations', 'ligand_protein_molar_ratio_range': [0, 6], 'pH': 7.4, 'protein_concentration_mM': 0.1, 'target_variant': 'Y18S'}
Qualification
Y18S mutant measurement; must not be pooled with wild-type affinity. Construct is the source HDGFRP2 PWWP expression fragment (1–93) carrying the stated mutation. Replicate number and titration-specific temperature are not independently specified.
 PMID:39031937 · 2024Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved
Original observation record
{
  "assay_construct_end": 93,
  "assay_construct_start": 1,
  "assay_context": "purified_mutant_domain",
  "assay_organism": "Homo sapiens",
  "assay_record_id": "PWWP5:ASSAY:0028",
  "assay_type": "NMR chemical-shift perturbation Kd",
  "assay_value_transferred_to_modeled_stereoisomers": false,
  "ccd_id": null,
  "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "compound_name": "BPP",
  "conditions": {
    "binding_model": "1:1 global fit of perturbed residues",
    "buffer": "HEPES-buffered saline; CSP subsection does not separately give HEPES/NaCl concentrations",
    "ligand_protein_molar_ratio_range": [
      0,
      6
    ],
    "pH": 7.4,
    "protein_concentration_mM": 0.1,
    "target_variant": "Y18S"
  },
  "domain": "PWWP1",
  "domain_id": "UP:Q7Z4V5:PWWP1",
  "endpoint": "Kd",
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Results; Figure 3D",
  "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981",
  "gene": "HDGFL2",
  "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": 7.4,
  "pdb_id": null,
  "preparation_id": "PREP:BPP",
  "protein_id": "UP:Q7Z4V5",
  "publication_year": 2024,
  "reference_id": "PMID:39031937",
  "remaining_uncertainty": "Y18S mutant measurement; must not be pooled with wild-type affinity. Construct is the source HDGFRP2 PWWP expression fragment (1\u201393) carrying the stated mutation. Replicate number and titration-specific temperature are not independently specified.",
  "replicates": null,
  "retrieval_date": "2026-10-26",
  "role": "experimentally_studied_ligand",
  "source_id": "P5:S:WEI2024",
  "source_reported_uncertainty": "0.02",
  "source_reported_units": "mM",
  "source_reported_value": "0.29",
  "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1\u20134 captions; original Supplementary Figure S2 was not retrieved",
  "target_variant": "Y18S",
  "uncertainty": 0.02,
  "uncertainty_type": "fitting error",
  "uncertainty_uM": 20.0,
  "unit_conversion": "mM \u00d7 1000 = \u00b5M",
  "units": "mM",
  "value": 0.29,
  "value_operator": "=",
  "value_uM": 290.0,
  "verification_level": "primary_source_verified",
  "version": "phase5.chemical_curation.1.1.0"
}
BPPPREP:BPPNegative / censored GLYR1 PWWP1
Construct not curatedHomo sapiens		 qualitativeBinding selectivity; assay method not verified in Figure S2qualitative binding Source reports non-detectable affinity in the tested selectivity comparison.
Experimental context
Replicates
Not curated
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
°C
Buffer
Not curated
Conditions
Not curated
Qualification
No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.
 PMID:39031937 · 2024Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved
Original observation record
{
  "assay_construct_end": null,
  "assay_construct_start": null,
  "assay_context": "purified_domain",
  "assay_organism": "Homo sapiens",
  "assay_record_id": "PWWP5:ASSAY:0029",
  "assay_type": "Binding selectivity; assay method not verified in Figure S2",
  "assay_value_transferred_to_modeled_stereoisomers": false,
  "ccd_id": null,
  "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "compound_name": "BPP",
  "conditions": {},
  "domain": "PWWP1",
  "domain_id": "UP:Q49A26:PWWP1",
  "endpoint": "qualitative",
  "evidence_class": "qualitative_binding",
  "evidence_location": "Results: selectivity paragraph referring to Figure S2",
  "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981",
  "gene": "GLYR1",
  "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.",
  "is_negative": true,
  "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.",
  "numeric_transcription_status": "qualitative_or_not_reported",
  "numeric_value_inferred_from_structure": false,
  "pdb_id": null,
  "preparation_id": "PREP:BPP",
  "protein_id": "UP:Q49A26",
  "publication_year": 2024,
  "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.",
  "reference_id": "PMID:39031937",
  "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.",
  "replicates": null,
  "retrieval_date": "2026-10-26",
  "role": "experimentally_studied_ligand",
  "source_id": "P5:S:WEI2024",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1\u20134 captions; original Supplementary Figure S2 was not retrieved",
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "units": null,
  "value": null,
  "value_operator": null,
  "value_uM": null,
  "verification_level": "primary_source_verified",
  "version": "phase5.chemical_curation.1.1.0"
}
BPPPREP:BPPNegative / censored BRPF1 PWWP1
Construct not curatedHomo sapiens		 qualitativeBinding selectivity; assay method not verified in Figure S2qualitative binding Source reports non-detectable affinity in the tested selectivity comparison.
Experimental context
Replicates
Not curated
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
°C
Buffer
Not curated
Conditions
Not curated
Qualification
No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.
 PMID:39031937 · 2024Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved
Original observation record
{
  "assay_construct_end": null,
  "assay_construct_start": null,
  "assay_context": "purified_domain",
  "assay_organism": "Homo sapiens",
  "assay_record_id": "PWWP5:ASSAY:0030",
  "assay_type": "Binding selectivity; assay method not verified in Figure S2",
  "assay_value_transferred_to_modeled_stereoisomers": false,
  "ccd_id": null,
  "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "compound_name": "BPP",
  "conditions": {},
  "domain": "PWWP1",
  "domain_id": "UP:P55201:PWWP1",
  "endpoint": "qualitative",
  "evidence_class": "qualitative_binding",
  "evidence_location": "Results: selectivity paragraph referring to Figure S2",
  "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981",
  "gene": "BRPF1",
  "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.",
  "is_negative": true,
  "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.",
  "numeric_transcription_status": "qualitative_or_not_reported",
  "numeric_value_inferred_from_structure": false,
  "pdb_id": null,
  "preparation_id": "PREP:BPP",
  "protein_id": "UP:P55201",
  "publication_year": 2024,
  "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.",
  "reference_id": "PMID:39031937",
  "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.",
  "replicates": null,
  "retrieval_date": "2026-10-26",
  "role": "experimentally_studied_ligand",
  "source_id": "P5:S:WEI2024",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1\u20134 captions; original Supplementary Figure S2 was not retrieved",
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "units": null,
  "value": null,
  "value_operator": null,
  "value_uM": null,
  "verification_level": "primary_source_verified",
  "version": "phase5.chemical_curation.1.1.0"
}
BPPPREP:BPPNegative / censored DNMT3B PWWP1
Construct not curatedHomo sapiens		 qualitativeBinding selectivity; assay method not verified in Figure S2qualitative binding Source reports non-detectable affinity in the tested selectivity comparison.
Experimental context
Replicates
Not curated
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
°C
Buffer
Not curated
Conditions
Not curated
Qualification
No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.
 PMID:39031937 · 2024Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved
Original observation record
{
  "assay_construct_end": null,
  "assay_construct_start": null,
  "assay_context": "purified_domain",
  "assay_organism": "Homo sapiens",
  "assay_record_id": "PWWP5:ASSAY:0031",
  "assay_type": "Binding selectivity; assay method not verified in Figure S2",
  "assay_value_transferred_to_modeled_stereoisomers": false,
  "ccd_id": null,
  "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "compound_name": "BPP",
  "conditions": {},
  "domain": "PWWP1",
  "domain_id": "UP:Q9UBC3:PWWP1",
  "endpoint": "qualitative",
  "evidence_class": "qualitative_binding",
  "evidence_location": "Results: selectivity paragraph referring to Figure S2",
  "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981",
  "gene": "DNMT3B",
  "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.",
  "is_negative": true,
  "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.",
  "numeric_transcription_status": "qualitative_or_not_reported",
  "numeric_value_inferred_from_structure": false,
  "pdb_id": null,
  "preparation_id": "PREP:BPP",
  "protein_id": "UP:Q9UBC3",
  "publication_year": 2024,
  "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.",
  "reference_id": "PMID:39031937",
  "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Protein has the named PWWP domain; this qualitative observation is not an unbounded inactivity claim.",
  "replicates": null,
  "retrieval_date": "2026-10-26",
  "role": "experimentally_studied_ligand",
  "source_id": "P5:S:WEI2024",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1\u20134 captions; original Supplementary Figure S2 was not retrieved",
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "units": null,
  "value": null,
  "value_operator": null,
  "value_uM": null,
  "verification_level": "primary_source_verified",
  "version": "phase5.chemical_curation.1.1.0"
}
BPPPREP:BPPNegative / censored NSD2 · PWWP instance unresolved
Construct not curatedHomo sapiens		 qualitativeBinding selectivity; assay method not verified in Figure S2qualitative binding Source reports non-detectable affinity in the tested selectivity comparison.
Experimental context
Replicates
Not curated
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
°C
Buffer
Not curated
Conditions
Not curated
Qualification
No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Source says NSD2 PWWP but does not specify PWWP1 versus PWWP2 in the inspected passage; domain_id remains null.
 PMID:39031937 · 2024Official publisher full HTML independently inspected: Methods, Results and Figures 1–4 captions; original Supplementary Figure S2 was not retrieved
Original observation record
{
  "assay_construct_end": null,
  "assay_construct_start": null,
  "assay_context": "purified_PWWP_domain_unspecified_instance",
  "assay_organism": "Homo sapiens",
  "assay_record_id": "PWWP5:ASSAY:0032",
  "assay_type": "Binding selectivity; assay method not verified in Figure S2",
  "assay_value_transferred_to_modeled_stereoisomers": false,
  "ccd_id": null,
  "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "compound_name": "BPP",
  "conditions": {},
  "domain": null,
  "domain_id": null,
  "endpoint": "qualitative",
  "evidence_class": "qualitative_binding",
  "evidence_location": "Results: selectivity paragraph referring to Figure S2",
  "evidence_url": "https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981",
  "gene": "NSD2",
  "inclusion_rationale": "Primary source explicitly identifies this preparation, target context and observation.",
  "is_negative": true,
  "negative_evidence_scope": "Non-detectable binding in the source experimental comparison; assay limits not recovered.",
  "numeric_transcription_status": "qualitative_or_not_reported",
  "numeric_value_inferred_from_structure": false,
  "pdb_id": null,
  "preparation_id": "PREP:BPP",
  "protein_id": "UP:O96028",
  "publication_year": 2024,
  "qualitative_result": "Source reports non-detectable affinity in the tested selectivity comparison.",
  "reference_id": "PMID:39031937",
  "remaining_uncertainty": "No concentration limit, numeric Kd, assay method or construct boundaries assigned without original Supplementary Figure S2. Source says NSD2 PWWP but does not specify PWWP1 versus PWWP2 in the inspected passage; domain_id remains null.",
  "replicates": null,
  "retrieval_date": "2026-10-26",
  "role": "experimentally_studied_ligand",
  "source_id": "P5:S:WEI2024",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "Official publisher full HTML independently inspected: Methods, Results and Figures 1\u20134 captions; original Supplementary Figure S2 was not retrieved",
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "units": null,
  "value": null,
  "value_operator": null,
  "value_uM": null,
  "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 / ligandNative domain & protein chainGeometric evidenceMinimum distanceInspect
8Z6C · A1D73PDB:8Z6C:LIG:D:A1D73:101:.HDGFL2 PWWP1Protein label chain A · ligand label chain Dnative annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.Core: 2.488 Å
Pfam: 2.488 Å		View deposited instance
8Z6C · A1D73PDB:8Z6C:LIG:D:A1D73:101:.HDGFL2 PWWP1Protein label chain C · ligand label chain Dnative annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.Core: 4.8102 Å
Pfam: 2.9842 Å		View deposited instance
8Z6C · A1D73PDB:8Z6C:LIG:G:A1D73:101:.HDGFL2 PWWP1Protein label chain B · ligand label chain Gnative annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.Core: 2.4923 Å
Pfam: 2.4923 Å		View deposited instance
8Z6C · A1D73PDB:8Z6C:LIG:J:A1D73:101:.HDGFL2 PWWP1Protein label chain C · ligand label chain Jnative annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.Core: 2.565 Å
Pfam: 2.565 Å		View deposited instance
9G94 · A1D73PDB:9G94:LIG:D:A1D73:101:.HDGFL2 PWWP1Protein label chain A · ligand label chain Dnative annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.Core: 2.2634 Å
Pfam: 2.2634 Å		View deposited instance
9G94 · A1D73PDB:9G94:LIG:G:A1D73:101:.HDGFL2 PWWP1Protein label chain A · ligand label chain Gnative annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.Core: 4.9223 Å
Pfam: 4.9223 Å		View deposited instance
9G94 · A1D73PDB:9G94:LIG:G:A1D73:101:.HDGFL2 PWWP1Protein label chain B · ligand label chain Gnative annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.Core: 2.4853 Å
Pfam: 2.4853 Å		View deposited instance
9G94 · A1D73PDB:9G94:LIG:J:A1D73:101:.HDGFL2 PWWP1Protein label chain C · ligand label chain Jnative annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.Core: 2.5415 Å
Pfam: 2.5415 Å		View deposited instance

Preparations, identities and controls remain separate

Experimental context

BPP

PREP:BPP

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

assay preparation
Complete preparation record
{
  "chemical_id": "INCHIKEY:LKKNQJJSEMQTHQ-UHFFFAOYSA-N",
  "entity_type": "small_molecule_preparation",
  "exact_ccd_id": "A1D73",
  "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": "BPP",
  "preparation_id": "PREP:BPP",
  "role": "assay_preparation",
  "sequence_if_defined": null
}

Provenance and reproducibility

Sources & downloads

https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14981https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14981https://www.rcsb.org/ligand/A1D73
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.