Research workbench
Potent inhibitors of NUDT5 silence hormone signaling in breast cancer
Analyse Potent inhibitors of NUDT5 silence hormone signaling in breast cancer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NQR
- Type
- protein
- Length
- 390 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-sugar pyrophosphatase
- EC
- 3.6.1.13, 3.6.1.58, 2.7.7.96
- UniProt
- Q9UKK9
- Ligands
- 958
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 195 | 23% helix, 44% strand | Q9UKK9 |
Ligands and binding sites
- 958 · 8-(dimethylamino)-1,3-dimethyl-7-[[5-(3-methylphenyl)-1,3,4-oxadiazol-2-yl]methyl]purine-2,6-dione · ligand · 3 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 | 310 | 0.71 | 0.84 | 40 | 958 |
| 2 | 328 | 0.71 | 0.84 | 40 | 958 |
| 3 | 71 | 0.31 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3123 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 5NQR · Potent inhibitors of NUDT5 silence hormone signaling in breast cancer · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9UKK9
- Elsewhere: RCSB PDB 5NQR · PDBe 5NQR · UniProt Q9UKK9
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