Structure of PDB 3lv8 Chain A Binding Site BS01

Receptor Information
>3lv8 Chain A (length=204) Species: 243277 (Vibrio cholerae O1 biovar El Tor str. N16961) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NAKFIVIEGLEGAGKSTAIQVVVETLQQNGIDHITRTREPGGTLLAEKLR
ALVKEEHPGEELQDITELLLVYAARVQLVENVIKPALARGEWVVGDRHDM
SSQAYQGGGRQIAPSTMQSLKQTALGDFKPDLTLYLDIDPKLGLERELDR
IEKMDISFFERARERYLELANSDDSVVMIDAAQSIEQVTADIRRALQDWL
SQVN
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 chain3lv8 Chain A Residue 213 [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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PDB3lv8 1.8 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with TMP, thymidine-5'-diphosphate and ADP
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G13 G15 K16 S17 R147 Q189 I191
Binding residue
(residue number reindexed from 1)		G12 G14 K15 S16 R146 Q183 I185
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.4.9: dTMP kinase.
Gene Ontology
Molecular Function
GO:0004712 protein serine/threonine/tyrosine kinase activity
GO:0004798 thymidylate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
Biological Process
GO:0006227 dUDP biosynthetic process
GO:0006233 dTDP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0016310 phosphorylation
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:3lv8, PDBe:3lv8, PDBj:3lv8
PDBsum3lv8
PubMed
UniProtQ9KQI2|KTHY_VIBCH Thymidylate kinase (Gene Name=tmk)

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