MolNFT v1 · #125989 · protein
Structure of NUDT15 in complex with 6-thio-gmp
5LPG · Probable 8-oxo-dgtp diphosphatase NUDT15: “Structure of NUDT15 in complex with 6-thio-gmp”. X-ray diffraction, 2 ligands (71V, MG), 3 pockets (best druggability 0.65). MolNFT v1 #125989 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5LPG
- Type
- protein
- Length
- 312 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 8-oxo-dgtp diphosphatase NUDT15
- EC
- 3.6.1.55
- UniProt
- Q9NV35
- Ligands
- 71V, MG
- Pockets
- 3 · best druggability 0.65
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 3.6.1.55) | protein | 156 | 21% helix, 36% strand | Q9NV35 |
Ligands and binding sites
- 71V · [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-sulfanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate · ligand · chains A
- MG · Magnesium ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.65 | 0.83 | 31 | MG, 71V |
| 2 | 166 | 0.61 | 0.84 | 31 | MG |
| 3 | 53 | 0.30 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1669 Ų buried · 24 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 5LPG · PDBe 5LPG · UniProt Q9NV35
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