Research workbench
Crystal structure of USP7 in complex with a potent, selective and reversible small-molecule inhibitor
Analyse Crystal structure of USP7 in complex with a potent, selective and reversible… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N9T
- Type
- protein
- Length
- 702 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
- 8QQ, SO4
- Pockets
- 10 · best druggability 0.70
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 | 357 | 34% helix, 26% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 345 | 33% helix, 28% strand | Q93009 |
Ligands and binding sites
- 8QQ · 3-[4-(aminomethyl)phenyl]-2-methyl-6-[[4-oxidanyl-1-[(3~{R})-4,4,4-tris(fluoranyl)-3-phenyl-butanoyl]piperidin-4-yl]methyl]pyrazolo[4,3-d]pyrimidin-7-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.70 | 0.86 | 24 | 8QQ |
| 2 | 214 | 0.70 | 0.86 | 24 | GOL, 8QQ |
| 3 | 225 | 0.54 | 0.78 | 40 | empty |
| 4 | 106 | 0.44 | 0.78 | 22 | SO4 |
| 5 | 124 | 0.41 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 680 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5N9T · Crystal structure of USP7 in complex with a potent, selective and reversible… · 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 5N9T · PDBe 5N9T · UniProt Q93009
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.