MolNFT v1 · #190645 · protein
Crystal structure of USP7 in complex with its inhibitor
7XPY · Ubiquitin carboxyl-terminal hydrolase 7: “Crystal structure of USP7 in complex with its inhibitor”. X-ray diffraction, 1 ligand (EIB), 8 pockets (best druggability 0.60). MolNFT v1 #190645 on GenesisL1: 3D structure, binding sites…
- PDB
- 7XPY
- Type
- protein
- Length
- 528 residues
- Chains
- 1
- 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
- EIB
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 528 | 23% helix, 34% strand | Q93009 |
Ligands and binding sites
- EIB · [(3s,3ar,4r,6z,9s,10e,11ar)-9-acetyloxy-6-(acetyloxymethyl)-3,10-dimethyl-2-oxidanylidene-3A,4, 5,8,9,11A-hexahydro-3H-cyclodeca[b]furan-4-yl] (E)-2-methyl-4-oxidanyl-but-2-enoate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.60 | 0.81 | 31 | empty |
| 2 | 110 | 0.52 | 0.82 | 18 | empty |
| 3 | 50 | 0.51 | 0.88 | 17 | empty |
| 4 | 210 | 0.47 | 0.74 | 34 | empty |
| 5 | 178 | 0.45 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7XPY · Crystal structure of USP7 in complex with its inhibitor · 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 7XPY · PDBe 7XPY · UniProt Q93009
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