MolNFT v1 · #167508 · protein
USP7 in complex with ligand compound 23
6VN3 · Ubiquitin carboxyl-terminal hydrolase 7: “USP7 in complex with ligand compound 23”. X-ray diffraction, 1 ligand (R3Y), 10 pockets (best druggability 0.69). MolNFT v1 #167508 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6VN3
- Type
- protein
- Length
- 667 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
- R3Y
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 329 | 35% helix, 27% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 338 | 36% helix, 27% strand | Q93009 |
Ligands and binding sites
- R3Y · 1-{[7-(5-chloro-2-{[(3R,4S)-4-fluoropyrrolidin-3-yl]oxy}-3-methylphenyl)thieno[3,2-b]pyridin-2-yl]methyl}-1H-pyrrole-2,5-dione · 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 | 214 | 0.69 | 0.86 | 23 | R3Y |
| 2 | 199 | 0.66 | 0.85 | 26 | R3Y |
| 3 | 411 | 0.65 | 0.79 | 29 | empty |
| 4 | 531 | 0.62 | 0.75 | 47 | empty |
| 5 | 132 | 0.44 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 476 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6VN3 · USP7 in complex with ligand compound 23 · 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 6VN3 · PDBe 6VN3 · UniProt Q93009
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