Scientific evidence classification · Phase 6A preserved + Phase 6B additions

PWWP Compounds
& Bioactivity

Explore experimentally studied preparations separately from deposited research ligands, buffers, ions and unresolved chemical evidence. Every role is source- and target-context specific.

Explore studied compounds Structural & Binding Landscape →

Different denominators · 26 October 2026

38studied preparation profiles · 26 baseline + 12 new

109profiles with PWWP research-ligand geometry

93source assay / association observations · 80 baseline + 13 new

Combined Phase 6A + Phase 6B denominators. These groups overlap; the 109 structurally source-tagged research ligands are unchanged. Deposited components and reagents are not automatically biochemical binders.

Search compounds & identifiersProteinEvidence view

Specific PWWP domainExact PWWP-proximal deposited siteChemical identity

Assay, source & experimental-context filters

Assay method Endpoint Reported relation Exact concentration min (µM)Exact concentration max (µM) Publication / source databasePublication yearAssay organismTested constructVerification status / scope Missing experimental detailAny associated PDB structure Inventory scopeSort

Assay filters must match the same observation. Concentration ranges require one endpoint and exact positive measurements; inequalities and qualitative findings remain searchable separately.

Phase 6B · source-reviewed additions (separate from the Phase 6A snapshot)

0 matching new observations · 0 preparations

Keep source-level IC50, Kd, and whole-protein DC50 separate; these records were not included in the original 80.

Filter all Phase 6B assay contexts

Preparation	Target scope	Original assay	Primary source
No Phase 6B additions match the selected observation-level filters. This does not erase existing Phase 6A observations.

Evidence classification · exact source records

11 matching profiles

2 matching assay / association observations. Counts here are profiles, not unique assay events or deposited ligand instances; views overlap.

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Preparation	Tested target & construct	Method / endpoint	Original observation	Conditions & uncertainty	Source & verification
Bis-TrisPREP:BIS-TRIS	DNMT3B PWWP Construct not curatedHomo sapiens	Qualitative / associationNo pharmacological activity assignedstructural occupancy association	No quantitative observation curated	Experimental context Replicates Not curated Uncertainty definition Not curated; do not assume SD or SEM Temperature — Buffer Crystallization reservoir contains 0.1 M Bis-Tris; not an affinity assay Conditions {} Qualification Pocket occupancy in high-concentration crystallization buffer is not evidence of potency.	PMID:21720545 · 2011local_primary_full_text_XML; Tables 1-2, crystallization methods and ligand Results inspected 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:0034", "assay_type": "No pharmacological activity assigned", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "resolve_missing_CCD_to_BTB; retain_buffer_role", "baseline_assay_record": 1, "baseline_original": "{\"assay_record_id\": \"PWWP:ASSAY:0034\", \"assay_type\": \"No pharmacological activity assigned\", \"ccd_id\": null, \"compound_name\": \"Bis-Tris\", \"conditions\": {}, \"domain\": \"PWWP\", \"evidence_location\": \"Results: Trimethylated lysine histone recognition; crystallization methods\", \"evidence_url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC3119473/\", \"gene\": \"DNMT3B\", \"interpretation\": \"Observed aromatic-cage occupancy by crystallization buffer. Do not classify as a validated pharmacological ligand.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"3QKJ\", \"reference_id\": \"PMID:21720545\", \"role\": \"crystallization_buffer\", \"uncertainty\": null, \"units\": null, \"value\": null, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}", "buffer": "Crystallization reservoir contains 0.1 M Bis-Tris; not an affinity assay", "ccd_id": "BTB", "ccd_mapping_source": null, "chemical_id": "INCHIKEY:OWMVSZAMULFTJU-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "Bis-Tris", "conditions": "{}", "crystallographic_component_ids": null, "domain": "PWWP", "domain_id": "UP:Q9UBC3:PWWP1", "endpoint_label_status": null, "evidence_class": "structural_occupancy_association", "evidence_location": "Results: Trimethylated lysine histone recognition; crystallization methods", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3119473/", "gene": "DNMT3B", "interpretation": "Observed aromatic-cage occupancy by crystallization buffer. Do not classify as a validated pharmacological ligand.", "molecular_entity_type": "buffer_additive", "numeric_transcription_status": "not_a_quantitative_affinity_record", "numeric_value_inferred_from_structure": 0, "pH": 6.5, "pdb_id": "3QKJ", "preparation_id": "PREP:BIS-TRIS", "protein_id": "UP:Q9UBC3", "qualitative_result": null, "reference_id": "PMID:21720545", "remaining_uncertainty": "Pocket occupancy in high-concentration crystallization buffer is not evidence of potency.", "replicates": null, "role": "crystallization_buffer", "source_component_url": null, "source_id": "S07", "source_reported_uncertainty": null, "source_reported_units": null, "source_reported_value": null, "source_verification_scope": "local_primary_full_text_XML; Tables 1-2, crystallization methods and ligand Results inspected", "temperature_C": null, "uncertainty": null, "uncertainty_type": null, "uncertainty_uM": null, "unit_conversion": null, "units": null, "value": null, "value_operator": null, "value_uM": null, "verification_level": "primary_full_text_sections_verified" }
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" }

Preparation

Tested target & construct

Method / endpoint

Original observation

Conditions & uncertainty

Source & verification

Bis-TrisPREP:BIS-TRIS

DNMT3B PWWP
Construct not curatedHomo sapiens

Qualitative / associationNo pharmacological activity assignedstructural occupancy association

No quantitative observation curated

Experimental context

Replicates: Not curated
Uncertainty definition: Not curated; do not assume SD or SEM
Temperature: —
Buffer: Crystallization reservoir contains 0.1 M Bis-Tris; not an affinity assay
Conditions: {}
Qualification: Pocket occupancy in high-concentration crystallization buffer is not evidence of potency.

PMID:21720545 · 2011local_primary_full_text_XML; Tables 1-2, crystallization methods and ligand Results inspected

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:0034",
  "assay_type": "No pharmacological activity assigned",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": "resolve_missing_CCD_to_BTB; retain_buffer_role",
  "baseline_assay_record": 1,
  "baseline_original": "{\"assay_record_id\": \"PWWP:ASSAY:0034\", \"assay_type\": \"No pharmacological activity assigned\", \"ccd_id\": null, \"compound_name\": \"Bis-Tris\", \"conditions\": {}, \"domain\": \"PWWP\", \"evidence_location\": \"Results: Trimethylated lysine histone recognition; crystallization methods\", \"evidence_url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC3119473/\", \"gene\": \"DNMT3B\", \"interpretation\": \"Observed aromatic-cage occupancy by crystallization buffer. Do not classify as a validated pharmacological ligand.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"3QKJ\", \"reference_id\": \"PMID:21720545\", \"role\": \"crystallization_buffer\", \"uncertainty\": null, \"units\": null, \"value\": null, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}",
  "buffer": "Crystallization reservoir contains 0.1 M Bis-Tris; not an affinity assay",
  "ccd_id": "BTB",
  "ccd_mapping_source": null,
  "chemical_id": "INCHIKEY:OWMVSZAMULFTJU-UHFFFAOYSA-N",
  "chemical_identity_status": "exact_single_CCD_identity",
  "component_context": null,
  "compound_name": "Bis-Tris",
  "conditions": "{}",
  "crystallographic_component_ids": null,
  "domain": "PWWP",
  "domain_id": "UP:Q9UBC3:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "structural_occupancy_association",
  "evidence_location": "Results: Trimethylated lysine histone recognition; crystallization methods",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3119473/",
  "gene": "DNMT3B",
  "interpretation": "Observed aromatic-cage occupancy by crystallization buffer. Do not classify as a validated pharmacological ligand.",
  "molecular_entity_type": "buffer_additive",
  "numeric_transcription_status": "not_a_quantitative_affinity_record",
  "numeric_value_inferred_from_structure": 0,
  "pH": 6.5,
  "pdb_id": "3QKJ",
  "preparation_id": "PREP:BIS-TRIS",
  "protein_id": "UP:Q9UBC3",
  "qualitative_result": null,
  "reference_id": "PMID:21720545",
  "remaining_uncertainty": "Pocket occupancy in high-concentration crystallization buffer is not evidence of potency.",
  "replicates": null,
  "role": "crystallization_buffer",
  "source_component_url": null,
  "source_id": "S07",
  "source_reported_uncertainty": null,
  "source_reported_units": null,
  "source_reported_value": null,
  "source_verification_scope": "local_primary_full_text_XML; Tables 1-2, crystallization methods and ligand Results inspected",
  "temperature_C": null,
  "uncertainty": null,
  "uncertainty_type": null,
  "uncertainty_uM": null,
  "unit_conversion": null,
  "units": null,
  "value": null,
  "value_operator": null,
  "value_uM": null,
  "verification_level": "primary_full_text_sections_verified"
}

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"
}

PWWP Compounds& Bioactivity

0 matching new observations · 0 preparations

11 matching profiles

PWWP Compounds
& Bioactivity