Research workbench
Drosophila melanogaster deoxyribonucleoside kinase successfully activates gemcitabine in transduced cancer cell lines
Analyse Drosophila melanogaster deoxyribonucleoside kinase successfully activates… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VPP
- Type
- protein
- Length
- 371 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside kinase
- EC
- 2.7.1.145
- UniProt
- Q9XZT6
- Ligands
- GEO, SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 189 | 51% helix, 15% strand | Q9XZT6 |
| B | Deoxynucleoside kinase (EC 2.7.1.145) | protein | 182 | 54% helix, 15% strand | Q9XZT6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.69 | 0.87 | 32 | GEO, SO4 |
| 2 | 200 | 0.67 | 0.85 | 33 | GEO, SO4 |
| 3 | 132 | 0.51 | 0.79 | 14 | empty |
| 4 | 64 | 0.39 | 0.79 | 22 | empty |
| 5 | 50 | 0.25 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1229 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2VPP · Drosophila melanogaster deoxyribonucleoside kinase successfully activates gemcitabine in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XZT6 · AlphaFold monomer V2.0 prediction for deoxynucleoside kinase (Q9XZT6) · 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 Q9XZT6
- Elsewhere: RCSB PDB 2VPP · PDBe 2VPP · UniProt Q9XZT6
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