Structure of PDB 3akc Chain A Binding Site BS01

Receptor Information
>3akc Chain A (length=208) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRGIVTIDGPSASGKSSVARRVAAALGVPYLSSGLLYRAAAFLALRAGVD
PGDEEGLLALLEGLGVRLLAQAEGNRVLADGEDLTSFLHTPEVDRVVSAV
ARLPGVRAWVNRRLKEVPPPFVAEGRDMGTAVFPEAAHKFYLTASPEVRA
WRRARERPQAYEEVLRDLLRRDERDKAQSAPAPDALVLDTGGMTLDEVVA
WVLAHIRR
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 chain3akc Chain A Residue 209 [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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PDB3akc The crystal structure of the tertiary complex of CMP kinase with a phosphoryl group acceptor and a donor from Thermus thermophilus HB8
Resolution1.65 Å
Binding residue
(original residue number in PDB)		S33 G34 Y37 R38 V97 A101 R107 R126 R153 R171 D175 Q178
Binding residue
(residue number reindexed from 1)		S33 G34 Y37 R38 V97 A101 R107 R126 R153 R171 D175 Q178
Annotation score4
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
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006220 pyrimidine nucleotide metabolic process
GO:0009058 biosynthetic process
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:3akc, PDBe:3akc, PDBj:3akc
PDBsum3akc
PubMed
UniProtQ5SL35|KCY_THET8 Cytidylate kinase (Gene Name=cmk)

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