73 profiles
Protein record
HDGFL2
Hepatoma-derived growth factor-related protein 2
Homo sapiens671 amino acidsannotation supported
1annotated core in HDGFL2
86PDB entries with observed PWWP1 coordinates
4model records for PWWP1
5frozen v1.2 assay / association records for PWWP1
Canonical sequence · Source-mapped regions
Protein domain architecture
PWWP annotation cores, other annotated regions, and deposited construct mappings share the canonical amino acid axis. The original Atlas PWWP intervals retain their source definitions.
PWWP annotation coreOther source annotationPredicted candidate, when present
0 additional source-supported regions · coordinates and evidence
UniProt feature coordinates accepted after exact canonical sequence identity check against the frozen Atlas. Source annotations can be inferred by sequence or curated from experiments; evidence codes remain attached. Other domain types link to their UniProt source because the Atlas records PWWP domains.
Deposited construct mapping
1 selected exampleColored segments map deposited polymer sequences to this canonical protein; dark segments have observed coordinates. Unmapped tags and engineered residues are not assigned canonical positions. These are not certified whole-fold boundaries.
Mapping and construct evidence
Deposited polymer length: 93 residues. Mapped sequence identity: 100.0%. no sequence difference detected by mapping; not proof of wild type.
PWWP1: 58 / 58 annotation-core Cα residues observed.
Frozen SIFTS aligned regions with construct-to-UniProt sequence comparison. Bars are mapped canonical segments; tags, insertions, and unmapped termini are not assigned canonical positions. PDB source.
One mapped example per native domain, preferring frozen experimental representatives; up to four distinct mapped intervals.
Validated isoform differences · 3 PWWP correspondence records
Only source-validated PWWP core correspondences from the frozen v1.2 isoform audit; other-domain architectures are not projected onto isoforms. Coordinates in the isoform column refer to the individual isoform sequence; deleted cores remain absent.
Viewing HDGFL2 PWWP1
Canonical annotation interval 7–64 · UniProtKB reviewed feature. annotation core; not a certified complete folded domain or pocket.
Alternative PWWP annotations and interval provenance
[
{
"end": 62,
"identifier": "SM00293",
"integrated_identifier": "IPR000313",
"model": "SM00293",
"name": "domain with conserved PWWP motif",
"representative": false,
"score": 3.1e-19,
"source": "smart",
"source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q7Z4V5/?page_size=200",
"start": 5
},
{
"end": 87,
"identifier": "IPR000313",
"integrated_identifier": null,
"model": null,
"name": "PWWP domain",
"representative": false,
"score": null,
"source": "interpro",
"source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q7Z4V5/?page_size=200",
"start": 5
},
{
"end": 88,
"identifier": "cd20149",
"integrated_identifier": null,
"model": "cd20149",
"name": "PWWP domain found in Hepatoma-derived growth factor-related protein 2 (HDGFL2)",
"representative": false,
"score": 1.87929e-60,
"source": "cdd",
"source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q7Z4V5/?page_size=200",
"start": 5
},
{
"end": 64,
"identifier": "PS50812",
"integrated_identifier": "IPR000313",
"model": "PS50812",
"name": "PWWP domain profile",
"representative": false,
"score": null,
"source": "profile",
"source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q7Z4V5/?page_size=200",
"start": 7
},
{
"end": 87,
"identifier": "PF00855",
"integrated_identifier": "IPR000313",
"model": "PF00855",
"name": "PWWP domain",
"representative": false,
"score": 5.8e-13,
"source": "pfam",
"source_url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/Q7Z4V5/?page_size=200",
"start": 8
}
]PWWP1 · source-classified Phase 6A evidence
Ligands & Bioactivity
75 chemical or preparation profiles · 7 domain-attributed assay / association observations. Counts refer to the curated snapshot.
0 profiles
Studied without research structure
No records in this category for the selected domain in the curated snapshot.
0 profiles
Experiment-specific controls
No records in this category for the selected domain in the curated snapshot.
2 profiles
Ambiguous / indirect evidence
H4K20me3 peptide / trimethyllysine monomer2 observations · 0 research-ligand entriesNbH101 observations · 0 research-ligand entries5 other deposited components in this domain (not pharmacological ligands)
Buffers, ions, cryoprotectants and solvents remain recorded as deposited chemical components.
DIMETHYL SULFOXIDE · Other PDB component · not a studied ligand1,2-ETHANEDIOL · Other PDB component · not a studied ligandGLYCEROL · Other PDB component · not a studied ligandSULFATE ION · Other PDB component · not a studied ligand(4S)-2-METHYL-2,4-PENTANEDIOL · Other PDB component · not a studied ligandPWWP1 · Deposited coordinates
Experimental coverage and AlphaFold correspondence
One representative chain per PDB entry and native domain. RMSD uses fixed UniProt correspondence and all common Cα atoms; it is reported only for ≥40 atoms and ≥80% core coverage. A value is descriptive, not a prediction benchmark.
| PDB | Chain | Observed core Cα | Class | Method / resolution | AF RMSD Å | Review |
|---|---|---|---|---|---|---|
| 3EAE | A | 58 / 58 | APO | X-RAY DIFFRACTION 2.24 Å | 1.14 | No classification flag |
| 3QBY | A | 58 / 58 | Complexes | X-RAY DIFFRACTION 1.95 Å | 0.837 | Required |
| 7HG0 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.58 Å | 0.807 | No classification flag |
| 7HG1 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.81 Å | 0.754 | No classification flag |
| 7HG2 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.7 Å | 0.747 | No classification flag |
| 7HG3 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.45 Å | 0.788 | No classification flag |
| 7HG4 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.57 Å | 0.721 | No classification flag |
| 7HG5 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.57 Å | 0.746 | No classification flag |
| 7HG6 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.52 Å | 0.727 | No classification flag |
| 7HG7 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.76 Å | 0.765 | No classification flag |
| 7HG8 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.67 Å | 0.752 | No classification flag |
| 7HG9 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.58 Å | 0.717 | No classification flag |
| 7HGA | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.57 Å | 0.762 | No classification flag |
| 7HGB | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.52 Å | 0.77 | No classification flag |
| 7HGC | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.51 Å | 0.762 | No classification flag |
| 7HGD | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.65 Å | 0.768 | No classification flag |
| 7HGE | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.77 Å | 0.801 | No classification flag |
| 7HGF | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.55 Å | 0.747 | No classification flag |
| 7HGG | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.61 Å | 0.716 | No classification flag |
| 7HGH | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.74 Å | 0.776 | No classification flag |
| 7HGI | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.71 Å | 0.725 | No classification flag |
| 7HGJ | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.75 Å | 0.777 | No classification flag |
| 7HGK | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.59 Å | 0.764 | No classification flag |
| 7HGL | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.73 Å | 0.718 | No classification flag |
| 7HGM | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.61 Å | 0.736 | No classification flag |
| 7HGN | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.55 Å | 0.79 | No classification flag |
| 7HGO | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.44 Å | 0.768 | No classification flag |
| 7HGP | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.62 Å | 0.738 | No classification flag |
| 7HGQ | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.76 Å | 0.819 | No classification flag |
| 7HGR | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.41 Å | 0.76 | No classification flag |
| 7HGS | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.51 Å | 0.771 | No classification flag |
| 7HGT | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.57 Å | 0.759 | No classification flag |
| 7HGU | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.67 Å | 0.784 | No classification flag |
| 7HGV | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.48 Å | 0.728 | No classification flag |
| 7HGW | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.59 Å | 0.731 | No classification flag |
| 7HGX | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.57 Å | 0.777 | No classification flag |
| 7HGY | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.61 Å | 0.75 | No classification flag |
| 7HGZ | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.65 Å | 0.762 | No classification flag |
| 7HH0 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.6 Å | 0.755 | No classification flag |
| 7HH1 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.53 Å | 0.764 | No classification flag |
| 7HH2 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.78 Å | 0.728 | No classification flag |
| 7HH3 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.64 Å | 0.764 | No classification flag |
| 7HH4 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.49 Å | 0.741 | No classification flag |
| 7HH5 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.66 Å | 0.754 | No classification flag |
| 7HH6 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.71 Å | 0.75 | No classification flag |
| 7HH7 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.73 Å | 0.758 | No classification flag |
| 7HH8 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.81 Å | 0.706 | No classification flag |
| 7HH9 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.54 Å | 0.732 | No classification flag |
| 7HHA | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.8 Å | 0.765 | No classification flag |
| 7HHB | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.78 Å | 0.755 | No classification flag |
| 7HHC | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.59 Å | 0.754 | No classification flag |
| 7HHD | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.57 Å | 0.721 | No classification flag |
| 7HHE | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 2.04 Å | 0.765 | No classification flag |
| 7HHF | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.86 Å | 0.697 | No classification flag |
| 7HHG | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.5 Å | 0.785 | No classification flag |
| 7HHH | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.69 Å | 0.782 | No classification flag |
| 7HHI | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 2.11 Å | 0.801 | No classification flag |
| 7HHJ | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.78 Å | 0.766 | No classification flag |
| 7HHK | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.94 Å | 0.798 | No classification flag |
| 7HHL | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.71 Å | 0.758 | No classification flag |
| 7HHM | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.78 Å | 0.75 | No classification flag |
| 7HHN | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.77 Å | 0.745 | No classification flag |
| 7HHO | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.76 Å | 0.722 | No classification flag |
| 7HHP | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.78 Å | 0.726 | No classification flag |
| 7HHQ | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.6 Å | 0.769 | No classification flag |
| 7HHR | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 2.03 Å | 0.798 | No classification flag |
| 8Z6C | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.93 Å | 0.702 | No classification flag |
| 8Z6O | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.55 Å | 1.36 | No classification flag |
| 9G91 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.78 Å | 0.666 | No classification flag |
| 9G94 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.73 Å | 0.802 | No classification flag |
| 9G96 | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.94 Å | 0.678 | No classification flag |
| 9GRS | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.66 Å | 0.806 | No classification flag |
| 9GRT | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.64 Å | 0.778 | No classification flag |
| 9GRU | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.7 Å | 0.713 | No classification flag |
| 9GRV | A | 58 / 58 | Co-Crystals | X-RAY DIFFRACTION 1.55 Å | 0.849 | No classification flag |
| 9I7A | A | 58 / 58 | APO | X-RAY DIFFRACTION 1.05 Å | 0.932 | No classification flag |
| 9I7B | A | 58 / 58 | APO | X-RAY DIFFRACTION 1.41 Å | 0.673 | No classification flag |
| 9I7C | A | 58 / 58 | APO | X-RAY DIFFRACTION 1.55 Å | 0.835 | No classification flag |
| 9I7E | A | 58 / 58 | APO | X-RAY DIFFRACTION 1.58 Å | 0.81 | No classification flag |
| 9I7F | C | 58 / 58 | APO | X-RAY DIFFRACTION 2.08 Å | 1.17 | No classification flag |
| 9I7G | A | 58 / 58 | APO | X-RAY DIFFRACTION 1.93 Å | 1.14 | No classification flag |
| 9I7H | A | 58 / 58 | APO | X-RAY DIFFRACTION 1.54 Å | 0.925 | No classification flag |
| 9I7I | A | 58 / 58 | APO | X-RAY DIFFRACTION 1.4 Å | 0.751 | No classification flag |
| 9I7J | A | 58 / 58 | APO | X-RAY DIFFRACTION 1.8 Å | 1.27 | No classification flag |
| 3QJ6 | A | 56 / 58 | Complexes | X-RAY DIFFRACTION 2.3 Å | 0.771 | Required |
| 9I7D | A | 53 / 58 | APO | X-RAY DIFFRACTION 2.36 Å | 0.412 | No classification flag |
PWWP1 · Measured preparations
Frozen v1.2 assay records
This retained table is the original source projection. The Phase 5 Ligands & Bioactivity section above includes added observations and reviewed target context. Values remain attached to their assay, construct and preparation. A crystal structure does not transfer affinity to another construct or stereoisomer. Assay pages preserve field-level source-verification states where reviewed; unreviewed null fields remain uncurated.
| Preparation / identity | Assay and result | Construct | Evidence and source |
|---|---|---|---|
| BPP exact single CCD identity | NMR chemical-shift perturbation Kd = 7.0 µM ± 5.0 direct binding affinity | 1–93 | PMID:39031937 primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved Intermediate-exchange NMR fit has large fitting error; ITC cross-validation reported, exact separate ITC number not extracted. Assay conditions and interpretation{"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"} Authors report intermediate-exchange limitations and additional ITC validation. This record preserves the NMR value and fitting error. |
| H4K20me3 peptide / trimethyllysine monomer defined modified peptide sequence not monomer identity | Fluorescence polarization binding Very weak; too weak to fit reliably qualitative weak binding | Uncurated | PMID:21720545 local_primary_full_text_XML_table_verified Assay conditions and interpretation{"sequence": "AKRHRK(me3)VLRDN"} Solution binding cannot be quantified from this record; structural occupancy separately linked to 3QBY. |
| H4K20me3 peptide / trimethyllysine monomer defined modified peptide sequence not monomer identity | X-ray structural association; no pharmacological activity assigned No verified numeric value structural occupancy association | Uncurated | PMID:21720545 local_primary_full_text_XML; Tables 1-2, crystallization methods and ligand Results inspected M3L has a polymer residue identity. 3QBY structural occupancy coexists with very weak unfittable solution affinity in Table 1. Assay conditions and 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. |
| NbH10 named macromolecule no full sequence identity | SPR apparent Kd = 81.2 nM ± 1.8 direct binding affinity | 1–93 | PMID:42194065 local_primary_full_text_XML_table_and_methods_verified Assay conditions and interpretation{"protein_construct": "HDGFL2 1–93", "replicates": 3, "uncertainty_type": "SD"} Apparent SPR affinity of a nanobody; not a small molecule or a solved nanobody–PWWP complex. |
| varenicline exact single CCD identity | NMR chemical-shift perturbation Kd = 250.0 µM ± 40.0 direct binding affinity | 1–93 | PMID:39031937 primary_publisher_selected_indexed_Results_and_Methods_passages; Figure S2 not independently retrieved Full assay buffer, temperature and incubation metadata not transcribed; null means uncurated, not absent. Assay conditions and interpretation{"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"} Converted from 0.25 ± 0.04 mM. Receptor pharmacology in other systems is not evidence of PWWP potency. |
PWWP1 · Prediction evidence
Predicted models
Domain retention uses independently reconstructed UniProt isoform edits. Local pLDDT is not experimental confirmation and does not establish interdomain orientation.
| Model | Origin | Core retention | Core mean pLDDT | Full mean pLDDT | Cautions |
|---|---|---|---|---|---|
| AF-Q7Z4V5-F1:v6 Canonical | GDM | complete | 88.8 | 59.9 | |
| AF-Q7Z4V5-2-F1:v6 | GDM | complete | 88.7 | 59.7 | |
| AF-Q7Z4V5-3-F1:v6 | GDM | complete | 88.8 | 60 | |
| AF-Q7Z4V5-4-F1:v6 | GDM | complete | 88.8 | 59.9 |
PWWP1 · Structural correspondence
Human annotation-core comparisons
Structural alignment establishes a residue correspondence for these cropped cores. It does not establish equivalent ligand pockets, function or selectivity.
| Domain pair | Aligned Cα | US-align RMSD Å | TM score A / B | View |
|---|---|---|---|---|
| ARID4A PWWP1 HDGFL2 PWWP1 | 58 | 1.71 | 0.541 / 0.802 | Aligned core viewer |
| BRD1 PWWP1 HDGFL2 PWWP1 | 58 | 2.48 | 0.56 / 0.766 | Aligned core viewer |
| BRPF1 PWWP1 HDGFL2 PWWP1 | 58 | 1.84 | 0.59 / 0.812 | Aligned core viewer |
| BRPF3 PWWP1 HDGFL2 PWWP1 | 58 | 1.77 | 0.585 / 0.799 | Aligned core viewer |
| DNMT3A PWWP1 HDGFL2 PWWP1 | 58 | 1.22 | 0.861 / 0.873 | Aligned core viewer |
| DNMT3B PWWP1 HDGFL2 PWWP1 | 58 | 1.19 | 0.863 / 0.876 | Aligned core viewer |
| HDGF PWWP1 HDGFL2 PWWP1 | 57 | 2.05 | 0.747 / 0.747 | Aligned core viewer |
| HDGFL2 PWWP1 HDGFL3 PWWP1 | 57 | 1.04 | 0.923 / 0.923 | Aligned core viewer |
| HDGFL2 PWWP1 MSH6 PWWP1 | 56 | 2.13 | 0.761 / 0.713 | Aligned core viewer |
| HDGFL2 PWWP1 NSD2 PWWP1 | 55 | 1.79 | 0.795 / 0.72 | Aligned core viewer |
| HDGFL2 PWWP1 NSD3 PWWP1 | 56 | 1.96 | 0.791 / 0.727 | Aligned core viewer |
| HDGFL2 PWWP1 NSD3 PWWP2 | 57 | 2.18 | 0.769 / 0.719 | Aligned core viewer |
| HDGFL2 PWWP1 PSIP1 PWWP1 | 57 | 1.75 | 0.801 / 0.739 | Aligned core viewer |
| HDGFL2 PWWP1 PWWP2B PWWP1 | 52 | 1.72 | 0.769 / 0.736 | Aligned core viewer |
| HDGFL2 PWWP1 PWWP3A PWWP1 | 51 | 2.23 | 0.68 / 0.645 | Aligned core viewer |
| HDGFL2 PWWP1 ZMYND11 PWWP1 | 51 | 2.08 | 0.687 / 0.747 | Aligned core viewer |
| HDGFL2 PWWP1 ZMYND8 PWWP1 | 51 | 2.01 | 0.689 / 0.762 | Aligned core viewer |