Download MendeleyFragment based discovery of small molecule inhibitors of the HDGFRP2 PWWP domain
Wei, X., Ruan, K.To be published.
8Z6O | pdb_00008z6o
Crystal structure of HDGFRP2 PWWP domain in complex with Varenicline
- PDB DOI: https://doi.org/10.2210/pdb8Z6O/pdb
- Classification: SIGNALING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-04-19 Released: 2025-04-23
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 ?
- R-Value Free: 0.214 (Depositor), 0.217 (DCC)
- R-Value Work: 0.187 (Depositor), 0.189 (DCC)
- R-Value Observed: 0.188 (Depositor)
Starting Model: experimental
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This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Hepatoma-derived growth factor-related protein 2 | 93 | Homo sapiens | Mutation(s): 0 Gene Names: HDGFL2, HDGF2, HDGFRP2, HRP2, UNQ785/PRO1604 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q7Z4V5 (Homo sapiens) Explore Q7Z4V5 Go to UniProtKB: Q7Z4V5 | |||||
GTEx: ENSG00000167674 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q7Z4V5 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| QMR (Subject of Investigation/LOI) Query on QMR | D [auth B] | VARENICLINE C13 H13 N3 JQSHBVHOMNKWFT-DTORHVGOSA-N |  | ||
| DMS (Subject of Investigation/LOI) Query on DMS | C [auth A] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 ?
- R-Value Free: 0.214 (Depositor), 0.217 (DCC)
- R-Value Work: 0.187 (Depositor), 0.189 (DCC)
- R-Value Observed: 0.188 (Depositor)
Space Group: P 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 35.054 | ¦Á = 63.16 |
| b = 39.012 | ¦Â = 70.31 |
| c = 41.72 | ¦Ă = 73.59 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
| PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 22377119 |
Revision History (Full details and data files)
- Version 1.0: 2025-04-23
Type: Initial release
