Structure of PDB 3fkb Chain D Binding Site BS01

Receptor Information
>3fkb Chain D (length=149) Species: 44689 (Dictyostelium discoideum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHY
AEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAPG
SIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE
Ligand information
Ligand IDTNV
InChIInChI=1S/C9H16N5O10P3/c1-6(2-14-4-13-7-8(10)11-3-12-9(7)14)22-5-25(15,16)23-27(20,21)24-26(17,18)19/h3-4,6H,2,5H2,1H3,(H,15,16)(H,20,21)(H2,10,11,12)(H2,17,18,19)/t6-/m1/s1
InChIKeyIACQCQDWSIQSRP-ZCFIWIBFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[C@H](Cn1cnc2c(N)ncnc12)OC[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.5.0C[C@H](Cn1cnc2c1ncnc2N)OC[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0CC(Cn1cnc2c1ncnc2N)OCP(=O)(O)OP(=O)(O)OP(=O)(O)O
CACTVS 3.341C[CH](Cn1cnc2c(N)ncnc12)OC[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O
FormulaC9 H16 N5 O10 P3
Name[2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE;
TENOFOVIR-DIPHOSPHATE
ChEMBLCHEMBL1236349
DrugBank
ZINCZINC000013516370
PDB chain3fkb Chain D Residue 160 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3fkb Nucleoside diphosphate kinase and the activation of antiviral phosphonate analogs of nucleotides: binding mode and phosphorylation of tenofovir derivatives
Resolution1.65 Å
Binding residue
(original residue number in PDB)		K16 Y56 H59 F64 R92 R109 V116
Binding residue
(residue number reindexed from 1)		K10 Y50 H53 F58 R86 R103 V110
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K16 Y56 N119 G122 E133
Catalytic site (residue number reindexed from 1) K10 Y50 N113 G116 E127
Enzyme Commision number 2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0004550 nucleoside diphosphate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006187 dGTP biosynthetic process from dGDP
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0006414 translational elongation
GO:0007186 G protein-coupled receptor signaling pathway
GO:0009117 nucleotide metabolic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0009617 response to bacterium
GO:0016310 phosphorylation
GO:0019954 asexual reproduction
GO:0030036 actin cytoskeleton organization
GO:0045920 negative regulation of exocytosis
GO:0048550 negative regulation of pinocytosis
GO:0050765 negative regulation of phagocytosis
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0015629 actin cytoskeleton
GO:0030141 secretory granule
GO:0045335 phagocytic vesicle

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3fkb, PDBe:3fkb, PDBj:3fkb
PDBsum3fkb
PubMed20183617
UniProtP22887|NDKC_DICDI Nucleoside diphosphate kinase, cytosolic (Gene Name=ndkC-1)

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