Structure of PDB 3akc Chain A Binding Site BS02

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 IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3akc Chain A Residue 210 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		A12 G14 K15 S16 S17 R152 R153 R155 E156 M193 T194 L195
Binding residue
(residue number reindexed from 1)		A12 G14 K15 S16 S17 R152 R153 R155 E156 M193 T194 L195
Annotation score5
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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