Research workbench
USP7 in complex with ligand compound 7
Analyse USP7 in complex with ligand compound 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VN5
- Type
- protein
- Length
- 677 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 7
- EC
- 3.4.19.12
- UniProt
- Q93009
- Ligands
- R41
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 337 | 33% helix, 27% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 340 | 33% helix, 27% strand | Q93009 |
Ligands and binding sites
- R41 · [(2R)-7-(2-aminopyridin-4-yl)-5-chloro-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.68 | 0.84 | 22 | R41 |
| 2 | 431 | 0.67 | 0.79 | 30 | empty |
| 3 | 247 | 0.66 | 0.83 | 25 | R41 |
| 4 | 697 | 0.66 | 0.75 | 56 | empty |
| 5 | 167 | 0.49 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 484 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6VN5 · USP7 in complex with ligand compound 7 · the same entry in another collection · chain A against A, TM-score 1.00
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 6VN5 · PDBe 6VN5 · UniProt Q93009
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