Research workbench
Crystal structure of USP7 in complex with the covalent inhibitor, FT827
Analyse Crystal structure of USP7 in complex with the covalent inhibitor, FT827 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NGF
- Type
- protein
- Length
- 664 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
- 8WN
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 332 | 34% helix, 27% strand | Q93009 |
Ligands and binding sites
- 8WN · ~{N}-[2-[4-[4-[(1-methyl-4-oxidanylidene-pyrazolo[3,4-d]pyrimidin-5-yl)methyl]-4-oxidanyl-piperidin-1-yl]carbonylphenyl]phenyl]ethanesulfonamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 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 | 605 | 0.69 | 0.78 | 61 | empty |
| 2 | 228 | 0.61 | 0.81 | 40 | 8WN |
| 3 | 207 | 0.57 | 0.79 | 28 | 8WN |
| 4 | 115 | 0.43 | 0.77 | 20 | empty |
| 5 | 90 | 0.39 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 193 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5NGF · Crystal structure of USP7 in complex with the covalent inhibitor, FT827 · 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 5NGF · PDBe 5NGF · UniProt Q93009
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