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Structure of PDB 1kdo Chain B Binding Site BS01

Receptor Information
>1kdo Chain B (length=223) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHV
DVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQ
VAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSE
ERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVL
DSTTLSIEQVIEKALQYARQKLA
Ligand information
Ligand IDC
InChIInChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyIERHLVCPSMICTF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H14 N3 O8 P
NameCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL307679
DrugBankDB03403
ZINCZINC000003861744
PDB chain1kdo Chain B Residue 6407 [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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PDB1kdo Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		S36 G37 Y40 R41 S101 A104 R110 R131 R181 D185 R188
Binding residue
(residue number reindexed from 1)		S34 G35 Y38 R39 S99 A102 R108 R129 R179 D183 R186
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.4.25: (d)CMP kinase.
Gene Ontology
Molecular Function
GO:0004127 (d)CMP kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0036430 CMP kinase activity
GO:0036431 dCMP kinase activity
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006220 pyrimidine nucleotide metabolic process
GO:0009058 biosynthetic process
GO:0010165 response to X-ray
GO:0015949 nucleobase-containing small molecule interconversion
GO:0016310 phosphorylation
GO:0044281 small molecule metabolic process
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1kdo, PDBe:1kdo, PDBj:1kdo
PDBsum1kdo
PubMed11827479
UniProtP0A6I0|KCY_ECOLI Cytidylate kinase (Gene Name=cmk)

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