Structure of PDB 3q89 Chain B Binding Site BS01

Receptor Information
>3q89 Chain B (length=149) Species: 93062 (Staphylococcus aureus subsp. aureus COL) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MERTFLMIKPDAVQRNLIGEVISRIERKGLKLVGGKLMQVPMELAETHYG
EHQGKPFYNDLISFITSAPVFAMVVEGEDAVNVSRHIIGSTNPSEASPGS
IRGDLGLTVGRNIIHGSDSLESAEREINLWFNENEITSYASPRDAWLYE
Ligand information
Ligand IDCDP
InChIInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyZWIADYZPOWUWEW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
FormulaC9 H15 N3 O11 P2
NameCYTIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL425252
DrugBankDB04555
ZINCZINC000008215624
PDB chain3q89 Chain B Residue 158 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3q89 Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		K9 H52 F57 T91 V109
Binding residue
(residue number reindexed from 1)		K9 H52 F57 T91 V109
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K9 Y49 N112 H115 E126
Catalytic site (residue number reindexed from 1) K9 Y49 N112 H115 E126
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:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0009117 nucleotide metabolic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0016310 phosphorylation
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3q89, PDBe:3q89, PDBj:3q89
PDBsum3q89
PubMed21745603
UniProtQ5HFV4|NDK_STAAC Nucleoside diphosphate kinase (Gene Name=ndk)

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