MolNFT v1 · #173636 · protein
Structure of NUDT15 V18_V19INSGV mutant in complex with TH7755
7B67 · Nucleotide triphosphate diphosphatase NUDT15: “Structure of NUDT15 V18_V19INSGV mutant in complex with TH7755”. X-ray diffraction, 3 ligands (SYW, MG, PO4), 2 pockets (best druggability 0.67). MolNFT v1 #173636 on GenesisL1: 3D…
- PDB
- 7B67
- Type
- protein
- Length
- 313 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotide triphosphate diphosphatase NUDT15
- EC
- 3.6.1.9
- UniProt
- Q9NV35
- Ligands
- SYW, MG, PO4
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleotide triphosphate diphosphatase NUDT15 (EC 3.6.1.9) | protein | 154 | 21% helix, 36% strand | Q9NV35 |
| B | Nucleotide triphosphate diphosphatase NUDT15 (EC 3.6.1.9) | protein | 159 | 21% helix, 35% strand | Q9NV35 |
Ligands and binding sites
- SYW · (R)-6-((2-methyl-4-(1-methyl-1H-indole-5-carbonyl) piperazin-1-yl)sulfonyl)benzo[d]oxazol-2(3H)-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.67 | 0.82 | 35 | SYW, PO4, MG |
| 2 | 256 | 0.64 | 0.82 | 30 | SYW |
Interfaces
1 interface between chains.
- A–B · 1574 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7B67 · Structure of NUDT15 V18_V19insGV Mutant in complex with TH7755 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NV35 · AlphaFold monomer V2.0 prediction for nucleotide triphosphate diphosphatase NUDT15… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 7B67 · PDBe 7B67 · UniProt Q9NV35
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