Research workbench
USP7 in complex with GNE6640 (4-(2-amino-4-ethyl-5-(1H-indazol-5-yl) pyridin-3-YL)PHENOL)
Analyse USP7 in complex with GNE6640 (4-(2-amino-4-ethyl-5-(1H-indazol-5-yl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UQV
- Type
- protein
- Length
- 658 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
- 8JM
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 329 | 31% helix, 26% strand | Q93009 |
Ligands and binding sites
- 8JM · 4-[2-amino-4-ethyl-5-(1H-indazol-5-yl)pyridin-3-yl]phenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.78 | 0.85 | 52 | empty |
| 2 | 437 | 0.65 | 0.78 | 45 | empty |
| 3 | 223 | 0.55 | 0.78 | 32 | empty |
| 4 | 245 | 0.52 | 0.76 | 29 | empty |
| 5 | 180 | 0.52 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 556 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5UQV · USP7 in complex with GNE6640 (4-(2-amino-4-ethyl-5-(1H-indazol-5-yl)pyridin-3-yl)phenol) · 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 5UQV · PDBe 5UQV · UniProt Q93009
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