Structure of PDB 1hiy Chain B Binding Site BS01

Receptor Information
>1hiy Chain B (length=150) Species: 44689 (Dictyostelium discoideum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESH
YAEHKERPFFGGLVSFITSGPVVAMVFEGKGVVASARLMIGVTNPLASAP
GSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE
Ligand information
Ligand ID3AN
InChIInChI=1S/C10H16N6O9P2/c11-5-4(1-23-27(21,22)25-26(18,19)20)24-10(7(5)17)16-3-15-6-8(12)13-2-14-9(6)16/h2-5,7,10,17H,1,11H2,(H,21,22)(H2,12,13,14)(H2,18,19,20)/t4-,5-,7-,10-/m1/s1
InChIKeyVKODIDNZKBYXJO-QYYRPYCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O)N)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)N)O)N
CACTVS 3.341N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P](O)(O)=O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3N
FormulaC10 H16 N6 O9 P2
Name3'-DEOXY 3'-AMINO ADENOSINE-5'-DIPHOSPHATE
ChEMBL
DrugBankDB04366
ZINCZINC000031976738
PDB chain1hiy Chain B Residue 1356 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1hiy Binding of Nucleotides to Nucleoside Diphosphate Kinase: A Calorimetric Study.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		H259 F264 L268 R292 T298 N319
Binding residue
(residue number reindexed from 1)		H54 F59 L63 R87 T93 N114
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=3.08,Kd=0.83mM
Enzymatic activity
Catalytic site (original residue number in PDB) K216 Y256 N319 H322 E333
Catalytic site (residue number reindexed from 1) K11 Y51 N114 H117 E128
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1hiy, PDBe:1hiy, PDBj:1hiy
PDBsum1hiy
PubMed11294625
UniProtP22887|NDKC_DICDI Nucleoside diphosphate kinase, cytosolic (Gene Name=ndkC-1)

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