MolNFT v1 · #167509 · protein
USP7 in complex with ligand compound 1
6VN4 · Ubiquitin carboxyl-terminal hydrolase 7: “USP7 in complex with ligand compound 1”. X-ray diffraction, 1 ligand (R4D), 7 pockets (best druggability 0.74). MolNFT v1 #167509 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6VN4
- Type
- protein
- Length
- 683 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
- R4D
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 341 | 34% helix, 26% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 342 | 34% helix, 26% strand | Q93009 |
Ligands and binding sites
- R4D · 3-({4-hydroxy-1-[(2R)-2-methyl-3-phenylpropanoyl]piperidin-4-yl}methyl)quinazolin-4(3H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.74 | 0.77 | 71 | empty |
| 2 | 204 | 0.72 | 0.88 | 23 | R4D |
| 3 | 189 | 0.69 | 0.87 | 24 | R4D |
| 4 | 297 | 0.55 | 0.76 | 29 | empty |
| 5 | 259 | 0.53 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 311 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6VN4 · USP7 in complex with ligand compound 1 · 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 6VN4 · PDBe 6VN4 · UniProt Q93009
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