MolNFT v1 · #173635 · protein
Structure of NUDT15 R139H mutant in complex with TH7755
7B66 · Nucleotide triphosphate diphosphatase NUDT15: “Structure of NUDT15 R139H mutant in complex with TH7755”. X-ray diffraction, 1 ligand (SYW), 5 pockets (best druggability 0.78). MolNFT v1 #173635 on GenesisL1: 3D structure, binding…
- PDB
- 7B66
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- 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
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleotide triphosphate diphosphatase NUDT15 (EC 3.6.1.9) | protein | 161 | 22% helix, 35% strand | Q9NV35 |
| B | Nucleotide triphosphate diphosphatase NUDT15 (EC 3.6.1.9) | protein | 155 | 21% helix, 36% strand | Q9NV35 |
| C | Nucleotide triphosphate diphosphatase NUDT15 (EC 3.6.1.9) | protein | 156 | 23% helix, 34% strand | Q9NV35 |
| D | Nucleotide triphosphate diphosphatase NUDT15 (EC 3.6.1.9) | protein | 156 | 21% helix, 36% 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 · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.78 | 0.80 | 117 | empty |
| 2 | 284 | 0.66 | 0.82 | 36 | SYW |
| 3 | 258 | 0.64 | 0.82 | 32 | SYW |
| 4 | 266 | 0.64 | 0.81 | 31 | SYW |
| 5 | 246 | 0.62 | 0.81 | 32 | SYW |
Interfaces
5 interfaces between chains.
- A–D · 1718 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1701 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 341 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 299 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7B66 · Structure of NUDT15 R139H Mutant in complex with TH7755 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NV35 · AlphaFold monomer V2.0 prediction for nucleotide triphosphate diphosphatase NUDT15… · a predicted model of the same protein · chain B 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 7B66 · PDBe 7B66 · UniProt Q9NV35
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