Research workbench
USP7 in complex with GNE6776 (6'-amino-4'-ethyl-5'-(4-hydroxyphenyl)- N-methyl-[3,3'-bipyridine]-6-carboxamide)
Analyse USP7 in complex with GNE6776 (6'-amino-4'-ethyl-5'-(4-hydroxyphenyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UQX
- Type
- protein
- Length
- 678 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
- 8JP
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 346 | 31% helix, 26% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 332 | 33% helix, 27% strand | Q93009 |
Ligands and binding sites
- 8JP · 6'-amino-4'-ethyl-5'-(4-hydroxyphenyl)-N-methyl[3,3'-bipyridine]-6-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.77 | 0.79 | 102 | empty |
| 2 | 127 | 0.50 | 0.80 | 16 | 8JP |
| 3 | 146 | 0.48 | 0.78 | 19 | empty |
| 4 | 98 | 0.45 | 0.79 | 17 | 8JP |
| 5 | 91 | 0.33 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 674 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5UQX · USP7 in complex with GNE6776 (6'-amino-4'-ethyl-5'-(4-hydroxyphenyl)-N-methyl-[3,3'-bipyri… · 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 5UQX · PDBe 5UQX · UniProt Q93009
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