MolNFT v1 · #128628 · protein
Potent inhibitors of NUDT5 silence hormone signaling in breast cancer
5NWH · ADP-sugar pyrophosphatase: “Potent inhibitors of NUDT5 silence hormone signaling in breast cancer”. X-ray diffraction, 1 ligand (9CH), 4 pockets (best druggability 0.73). MolNFT v1 #128628 on GenesisL1: 3D structure, binding sites…
- PDB
- 5NWH
- Type
- protein
- Length
- 388 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
- 9CH
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 193 | 20% helix, 42% strand | Q9UKK9 |
| B | ADP-sugar pyrophosphatase (EC 3.6.1.13, 3.6.1.58, 2.7.7.96) | protein | 195 | 20% helix, 43% strand | Q9UKK9 |
Ligands and binding sites
- 9CH · 7-[[5-(3,4-dichlorophenyl)-1,3,4-oxadiazol-2-yl]methyl]-1,3-dimethyl-8-piperazin-1-yl-purine-2,6-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.73 | 0.84 | 40 | 9CH |
| 2 | 386 | 0.73 | 0.84 | 49 | 9CH |
| 3 | 96 | 0.38 | 0.76 | 27 | empty |
| 4 | 50 | 0.23 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3190 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 5NWH · 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 5NWH · PDBe 5NWH · UniProt Q9UKK9
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