Research workbench
Crystal structure of USP7 in complex with a 4-hydroxypiperidine based inhibitor
Analyse Crystal structure of USP7 in complex with a 4-hydroxypiperidine based inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F5H
- Type
- protein
- Length
- 687 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
- CQ5, SO4
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 350 | 35% helix, 27% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 337 | 34% helix, 27% strand | Q93009 |
Ligands and binding sites
- CQ5 · 3-[[4-oxidanyl-1-[(3~{R})-3-phenylbutanoyl]piperidin-4-yl]methyl]-6-(2-pyrrolidin-1-ylethylamino)pyrimidin-4-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.73 | 0.90 | 22 | CQ5 |
| 2 | 182 | 0.71 | 0.89 | 25 | CQ5 |
| 3 | 177 | 0.52 | 0.78 | 26 | empty |
| 4 | 116 | 0.44 | 0.77 | 22 | empty |
| 5 | 117 | 0.40 | 0.75 | 19 | SO4 |
Interfaces
1 interface between chains.
- A–B · 674 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6F5H · Crystal structure of USP7 in complex with a 4-hydroxypiperidine based inhibitor · 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 6F5H · PDBe 6F5H · UniProt Q93009
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