Structure of PDB 1mn9 Chain B Binding Site BS01

Receptor Information
>1mn9 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
GSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE
Ligand information
Ligand IDRTP
InChIInChI=1S/C8H15N4O14P3/c9-6(15)7-10-2-12(11-7)8-5(14)4(13)3(24-8)1-23-28(19,20)26-29(21,22)25-27(16,17)18/h2-5,8,13-14H,1H2,(H2,9,15)(H,19,20)(H,21,22)(H2,16,17,18)/t3-,4-,5-,8-/m1/s1
InChIKeyMMJOCKKLRMRSEQ-AFCXAGJDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ncn(n1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
CACTVS 3.341NC(=O)c1ncn(n1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1nc(nn1C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)C(=O)N
OpenEye OEToolkits 1.5.0c1nc(nn1[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)C(=O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(n1nc(nc1)C(=O)N)C(O)C2O
FormulaC8 H15 N4 O14 P3
NameRIBAVIRIN TRIPHOSPHATE
ChEMBLCHEMBL398463
DrugBank
ZINCZINC000012402860
PDB chain1mn9 Chain A Residue 161 [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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PDB1mn9 Structural Analysis of the Activation of Ribavirin Analogs by NDP Kinase: Comparison with Other Ribavirin Targets
Resolution2.9 Å
Binding residue
(original residue number in PDB)		K16 Y56 H59 F64 L68 R92 T98 R109 V116 N119 G122 G123
Binding residue
(residue number reindexed from 1)		K11 Y51 H54 F59 L63 R87 T93 R104 V111 N114 G117 G118
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=4.62,Kd=24uM
Enzymatic activity
Catalytic site (original residue number in PDB) K16 Y56 N119 G122 E133
Catalytic site (residue number reindexed from 1) K11 Y51 N114 G117 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:1mn9, PDBe:1mn9, PDBj:1mn9
PDBsum1mn9
PubMed12606760
UniProtP22887|NDKC_DICDI Nucleoside diphosphate kinase, cytosolic (Gene Name=ndkC-1)

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