PDB Entry (2vpp)

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Visualizer: MichelaNGLo

PDB ID: 2vpp Resolution: 2.2 Å Exp. Method: X-RAY DIFFRACTION
PMID: 19285960 DOI: 10.1016/j.bbrc.2009.03.041
Protein
Protein Name: Deoxynucleoside kinase
Protein Class: TRANSFERASE
Uniprot ID/ACC: Q9XZT6 (DNK_DROME) Organism: Drosophila melanogaster
Gene Symbol: dnk Gene ID: 42273
Pocket Descriptors
Volume: 754.944 Depth: 22.9539
Hydrophobicity: 0.718954 Drug Score: 0.561358
Pocket Similarity: Calculate
Ligand
Ligand Name:   GEMCITABINE
HET ID:   GEO PubChem:   60750
DrugBank:   DB00441 ChEMBL:   CHEMBL888
Canonical SMILES:   OC[C@H]1O[C@H](C([C@@H]1O)(F)F)n1ccc(nc1=O)N
Standard InChI:   InChI=1S/C9H11F2N3O4/c10-9(11)6(16)4(3-15)18-7(9)14-2-1-5(12)13-8(14)17/h1-2,4,6-7,15-16H,3H2,(H2,12,13,17)/t4-,6-,7-/m1/s1
Molecular Formula:   C9H11F2N3O4 Mol. Weight:   263.19815 Heavy Atoms:   18
Charge:   0 Is Chiral:   True logP:   -0.7074
HBD:   3 HBA:   7 TPSA:   110.6
#Bonds:   22 #Rotatable Bonds:   2 Shape Complexity:   0.5555556
Stereocomplexity:   0.33333334 Ligand Type:   Small Molecule
Binding Affinity
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