MolNFT v1 · #128096 · protein
Crystal structure of USP7 in complex with the non-covalent inhibitor, FT671
5NGE · Ubiquitin carboxyl-terminal hydrolase 7: “Crystal structure of USP7 in complex with the non-covalent inhibitor, FT671”. X-ray diffraction, 1 ligand (8WK), 7 pockets (best druggability 0.71). MolNFT v1 #128096 on GenesisL1: 3D…
- PDB
- 5NGE
- Type
- protein
- Length
- 650 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
- 8WK
- Pockets
- 7 · best druggability 0.71
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 | 337 | 35% helix, 27% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 313 | 33% helix, 24% strand | Q93009 |
Ligands and binding sites
- 8WK · 5-[[1-[(3~{S})-4,4-bis(fluoranyl)-3-(3-fluoranylpyrazol-1-yl)butanoyl]-4-oxidanyl-piperidin-4-yl]methyl]-1-(4-fluorophenyl)pyrazolo[3,4-d]pyrimidin-4-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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.71 | 0.88 | 22 | 8WK |
| 2 | 188 | 0.69 | 0.87 | 24 | 8WK |
| 3 | 865 | 0.69 | 0.75 | 75 | empty |
| 4 | 104 | 0.38 | 0.75 | 19 | empty |
| 5 | 101 | 0.37 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 158 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5NGE · Crystal structure of USP7 in complex with the non-covalent inhibitor, FT671 · 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 5NGE · PDBe 5NGE · UniProt Q93009
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