Research workbench
Structure of NUDT15 in complex with inhibitor TH1760
Analyse Structure of NUDT15 in complex with inhibitor TH1760 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T5J
- Type
- protein
- Length
- 308 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
- MKB, MG, CL
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable 8-oxo-dgtp diphosphatase NUDT15 (EC 3.6.1.9) | protein | 154 | 21% helix, 36% strand | Q9NV35 |
Ligands and binding sites
- MKB · 6-[4-(1~{H}-indol-5-ylcarbonyl)piperazin-1-yl]sulfonyl-3~{H}-1,3-benzoxazol-2-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.62 | 0.84 | 22 | MKB |
| 2 | 191 | 0.60 | 0.82 | 21 | MKB |
| 3 | 72 | 0.39 | 0.79 | 25 | empty |
| 4 | 74 | 0.39 | 0.78 | 26 | empty |
| 5 | 59 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1664 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6T5J · Structure of NUDT15 in complex with inhibitor TH1760 · 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 6T5J · PDBe 6T5J · UniProt Q9NV35
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