MolNFT v1 · #127880 · protein
Crystal structure of USP7 in complex with a potent, selective and reversible small-molecule inhibitor
5N9R · Ubiquitin carboxyl-terminal hydrolase 7: “Crystal structure of USP7 in complex with a potent, selective and reversible small-molecule inhibitor”. X-ray diffraction, 2 ligands (8RN, SO4), 9 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 5N9R
- Type
- protein
- Length
- 703 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
- 8RN, SO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 356 | 37% helix, 27% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 347 | 34% helix, 27% strand | Q93009 |
Ligands and binding sites
- 8RN · 7-bromanyl-3-[[4-oxidanyl-1-[(3~{R})-3-phenylbutanoyl]piperidin-4-yl]methyl]thieno[3,2-d]pyrimidin-4-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.71 | 0.88 | 23 | DMS, 8RN |
| 2 | 209 | 0.71 | 0.87 | 25 | 8RN |
| 3 | 170 | 0.50 | 0.78 | 24 | empty |
| 4 | 167 | 0.49 | 0.77 | 34 | empty |
| 5 | 97 | 0.45 | 0.79 | 19 | SO4 |
Interfaces
1 interface between chains.
- A–B · 697 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5N9R · 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 5N9R · PDBe 5N9R · UniProt Q93009
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.