Structure of PDB 1s5z Chain A Binding Site BS01

Receptor Information
>1s5z Chain A (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 IDSON
InChIInChI=1S/C12H16N5O8P/c13-10-7-11(15-3-14-10)17(4-16-7)12-9(20)8(19)5(25-12)1-24-6(18)2-26(21,22)23/h3-5,8-9,12,19-20H,1-2H2,(H2,13,14,15)(H2,21,22,23)/t5-,8-,9-,12-/m1/s1
InChIKeyKJNLSEOJEFDELT-JJNLEZRASA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)CC(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COC(=O)CP(=O)(O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COC(=O)CP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](COC(=O)C[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](COC(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC12 H16 N5 O8 P
NameADENOSINE PHOSPHONOACETIC ACID
ChEMBLCHEMBL1236003
DrugBankDB02607
ZINCZINC000016051493
PDB chain1s5z Chain A Residue 1160 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1s5z Adenosine phosphonoacetic acid is slowly metabolized by NDP kinase.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		K16 H59 F64 T98 R109 V116 N119
Binding residue
(residue number reindexed from 1)		K11 H54 F59 T93 R104 V111 N114
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=3.21,Kd=0.62mM
Enzymatic activity
Catalytic site (original residue number in PDB) K16 Y56 N119 H122 E133
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1s5z, PDBe:1s5z, PDBj:1s5z
PDBsum1s5z
PubMed16787337
UniProtP22887|NDKC_DICDI Nucleoside diphosphate kinase, cytosolic (Gene Name=ndkC-1)

[Back to BioLiP]