Research workbench
USP7 in complex with Cpd2 (4-(3-(1-methylpiperidin-4-yl)-1,2,4-oxadiazol-5-yl)phenol)
Analyse USP7 in complex with Cpd2 (4-(3-(1-methylpiperidin-4-yl)-1,2,4-oxadiazol-5-yl)ph… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WHC
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.548
- Source
- Homo sapiens
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 7
- EC
- 3.4.19.12
- UniProt
- Q93009
- Ligands
- AJJ
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.548 · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 338 | 33% helix, 27% strand | Q93009 |
Ligands and binding sites
- AJJ · 4-[3-(1-methylpiperidin-4-yl)-1,2,4-oxadiazol-5-yl]phenol · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.65 | 0.87 | 26 | GOL |
| 2 | 439 | 0.64 | 0.77 | 45 | GOL |
| 3 | 205 | 0.54 | 0.79 | 35 | empty |
| 4 | 62 | 0.47 | 0.84 | 13 | AJJ |
| 5 | 147 | 0.44 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5WHC · USP7 in complex with CPD2 (4-(3-(1-methylpiperidin-4-yl)-1,2,4- oxadiazol-5-YL)PHENOL) · the same entry in another collection · chain A against A, TM-score 1.00
- Q93009 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 7 (Q93009) · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q93009
- Elsewhere: RCSB PDB 5WHC · PDBe 5WHC · UniProt Q93009
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