Research workbench
USP7 in complex with ligand compound 14
Analyse USP7 in complex with ligand compound 14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VN6
- Type
- protein
- Length
- 672 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
- R4J, ZN
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 335 | 32% helix, 28% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 337 | 31% helix, 28% strand | Q93009 |
Ligands and binding sites
- R4J · [(2R)-5-chloro-7-{2-[(2S)-1-chloro-2,3-dihydroxypropan-2-yl]thieno[3,2-b]pyridin-7-yl}-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.66 | 0.83 | 27 | R4J |
| 2 | 266 | 0.66 | 0.82 | 27 | R4J |
| 3 | 408 | 0.65 | 0.79 | 30 | empty |
| 4 | 584 | 0.64 | 0.75 | 57 | empty |
| 5 | 73 | 0.42 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 468 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6VN6 · USP7 in complex with ligand compound 14 · 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 6VN6 · PDBe 6VN6 · UniProt Q93009
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