MolNFT v1 · #183470 · protein
Structure of NUDT15 in complex with NSC56456
7NR6 · Probable 8-oxo-dgtp diphosphatase NUDT15: “Structure of NUDT15 in complex with NSC56456”. X-ray diffraction, 2 ligands (UO8, MG), 4 pockets (best druggability 0.65). MolNFT v1 #183470 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7NR6
- Type
- protein
- Length
- 306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 8-oxo-dgtp diphosphatase NUDT15
- EC
- 3.6.1.9
- UniProt
- Q9NV35
- Ligands
- UO8, MG
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable 8-oxo-dgtp diphosphatase NUDT15 (EC 3.6.1.9) | protein | 153 | 22% helix, 37% strand | Q9NV35 |
Ligands and binding sites
- UO8 · 2-azanyl-9-cyclohexyl-3~{H}-purine-6-thione · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.65 | 0.82 | 34 | MG, UO8 |
| 2 | 213 | 0.65 | 0.84 | 35 | MG, UO8 |
| 3 | 83 | 0.32 | 0.74 | 17 | empty |
| 4 | 69 | 0.30 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1643 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
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 Q9NV35
- Elsewhere: RCSB PDB 7NR6 · PDBe 7NR6 · UniProt Q9NV35
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