PWWPAtlas
STRUCTURAL BIOLOGY & CHEMICAL EVIDENCEDataset v1.2 · Phase 6D · Comparative experimental recognition environments
Experimental preparationIdentity not assigned

Measurements remain attached to the reported preparation.

Reported experimental preparation

H4K20me3 peptide / trimethyllysine monomer

Identity / evidence review pendingPreparation identity unresolved

M3L is one covalently linked residue, not the assayed peptide chemical identity.

HDGFL2 PWWP1
2 assay / association records1 preparations0 research-ligand PDB entries

No deposited PWWP research-ligand geometry is classified for this preparation in the selected release. Deposition of a buffer/ion is not binding evidence.

Clinical / development status: Not independently curated. A chemical probe classification does not imply medicinal approval.

Identity is separate from preparation

Chemical identity

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
H4K20me3 peptide / trimethyllysine monomerPREP:H4K20me3_11mer HDGFL2 PWWP
Construct not curatedHomo sapiens		 Qualitative / associationX-ray structural association; no 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
Not curated
Conditions
{}
Qualification
M3L has a polymer residue identity. 3QBY structural occupancy coexists with very weak unfittable solution affinity in Table 1.
 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:0036",
  "assay_type": "X-ray structural association; no pharmacological activity assigned",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": "separate_whole_peptide_preparation_from_M3L_monomer",
  "baseline_assay_record": 1,
  "baseline_original": "{\"assay_record_id\": \"PWWP:ASSAY:0036\", \"assay_type\": \"X-ray structural association; no pharmacological activity assigned\", \"ccd_id\": \"M3L\", \"component_context\": \"nonstandard_polymer_monomer\", \"compound_name\": \"H4K20me3 peptide / trimethyllysine monomer\", \"conditions\": {}, \"domain\": \"PWWP\", \"evidence_location\": \"Table 2; RCSB polymer entity 2\", \"evidence_url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC3119473/\", \"gene\": \"HDGFL2\", \"interpretation\": \"Chain H is an 11-residue H4K20me3 peptide AKRHR(M3L)VLRDN. M3L is a modified polymer monomer, not a free drug. The modeled subset must be distinguished from the full deposited peptide.\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"3QBY\", \"reference_id\": \"PMID:21720545\", \"role\": \"histone methyllysine surrogate/partially resolved peptide\", \"source_component_url\": \"https://data.rcsb.org/rest/v1/core/polymer_entity/3QBY/2\", \"uncertainty\": null, \"units\": null, \"value\": null, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}",
  "buffer": null,
  "ccd_id": "M3L",
  "ccd_mapping_source": null,
  "chemical_id": null,
  "chemical_identity_status": "defined_modified_peptide_sequence_not_monomer_identity",
  "component_context": "nonstandard_polymer_monomer",
  "compound_name": "H4K20me3 peptide / trimethyllysine monomer",
  "conditions": "{}",
  "crystallographic_component_ids": null,
  "domain": "PWWP",
  "domain_id": "UP:Q7Z4V5:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "structural_occupancy_association",
  "evidence_location": "Table 2; RCSB polymer entity 2",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3119473/",
  "gene": "HDGFL2",
  "interpretation": "Chain H is an 11-residue H4K20me3 peptide AKRHR(M3L)VLRDN. M3L is a modified polymer monomer, not a free drug. The modeled subset must be distinguished from the full deposited peptide.",
  "molecular_entity_type": "modified_histone_peptide",
  "numeric_transcription_status": "not_a_quantitative_affinity_record",
  "numeric_value_inferred_from_structure": 0,
  "pH": null,
  "pdb_id": "3QBY",
  "preparation_id": "PREP:H4K20me3_11mer",
  "protein_id": "UP:Q7Z4V5",
  "qualitative_result": null,
  "reference_id": "PMID:21720545",
  "remaining_uncertainty": "M3L has a polymer residue identity. 3QBY structural occupancy coexists with very weak unfittable solution affinity in Table 1.",
  "replicates": null,
  "role": "histone methyllysine surrogate/partially resolved peptide",
  "source_component_url": "https://data.rcsb.org/rest/v1/core/polymer_entity/3QBY/2",
  "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"
}
H4K20me3 peptide / trimethyllysine monomerPREP:H4K20me3_11mer HDGFL2 PWWP1
Construct not curatedHomo sapiens		 Qualitative / associationFluorescence polarization bindingqualitative weak binding Very weak; too weak to fit reliably
Experimental context
Replicates
Not curated
Uncertainty definition
Not curated; do not assume SD or SEM
Temperature
—
Buffer
Not curated
Conditions
{"sequence": "AKRHRK(me3)VLRDN"}
Qualification
Solution binding cannot be quantified from this record; structural occupancy separately linked to 3QBY.
 PMID:21720545 · 2011local_primary_full_text_XML_table_verified
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": "PWWP11:ASSAY:0010",
  "assay_type": "Fluorescence polarization binding",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": null,
  "baseline_assay_record": 0,
  "baseline_original": null,
  "buffer": null,
  "ccd_id": null,
  "ccd_mapping_source": null,
  "chemical_id": null,
  "chemical_identity_status": "defined_modified_peptide_sequence_not_monomer_identity",
  "component_context": null,
  "compound_name": "H4K20me3 peptide / trimethyllysine monomer",
  "conditions": "{\"sequence\": \"AKRHRK(me3)VLRDN\"}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:Q7Z4V5:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "qualitative_weak_binding",
  "evidence_location": "Table 1 H4K20me3 / HDGF2 cell and footnote",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3119473/",
  "gene": "HDGFL2",
  "interpretation": "Solution binding cannot be quantified from this record; structural occupancy separately linked to 3QBY.",
  "molecular_entity_type": "modified_histone_peptide",
  "numeric_transcription_status": "null_preserved_for_unfittable_binding",
  "numeric_value_inferred_from_structure": null,
  "pH": null,
  "pdb_id": "3QBY",
  "preparation_id": "PREP:H4K20me3_11mer",
  "protein_id": "UP:Q7Z4V5",
  "qualitative_result": "Very weak; too weak to fit reliably",
  "reference_id": "PMID:21720545",
  "remaining_uncertainty": null,
  "replicates": null,
  "role": "histone_peptide_assay",
  "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_table_verified",
  "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": 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: 3QBY

Preparations, identities and controls remain separate

Experimental context

H4K20me3 peptide / trimethyllysine monomer

PREP:H4K20me3_11mer

M3L is one covalently linked residue, not the assayed peptide chemical identity.

histone peptide
Complete preparation record
{
  "chemical_id": null,
  "entity_type": "modified_histone_peptide",
  "exact_ccd_id": null,
  "identity_note": "M3L is one covalently linked residue, not the assayed peptide chemical identity.",
  "identity_status": "defined_modified_peptide_sequence_not_monomer_identity",
  "modeled_candidate_ccd_ids": "[]",
  "modeled_candidate_chemical_ids": "[]",
  "name": "H4K20me3 peptide / trimethyllysine monomer",
  "preparation_id": "PREP:H4K20me3_11mer",
  "role": "histone_peptide",
  "sequence_if_defined": "AKRHRK(me3)VLRDN"
}

Provenance and reproducibility

Sources & downloads

https://pmc.ncbi.nlm.nih.gov/articles/PMC3119473/
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.