Structure of PDB 2ccj Chain A Binding Site BS01

Receptor Information
>2ccj Chain A (length=196) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIV
LEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQ
GYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNSNRLDQ
EDLKFHEKVIEGYQEIIHRFKSVNADQPLENVVEDTYQTIIKYLEK
Ligand information
Ligand IDTMP
InChIInChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyGYOZYWVXFNDGLU-XLPZGREQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
FormulaC10 H15 N2 O8 P
NameTHYMIDINE-5'-PHOSPHATE
ChEMBLCHEMBL394429
DrugBankDB01643
ZINCZINC000001678872
PDB chain2ccj Chain A Residue 1209 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2ccj Structures of S. Aureus Thymidylate Kinase Reveal an Atypical Active Site Configuration and an Intermediate Conformational State Upon Substrate Binding
Resolution1.7 Å
Binding residue
(original residue number in PDB)		K15 F66 R70 R92 S96 S97 Y100 Q101
Binding residue
(residue number reindexed from 1)		K14 F65 R69 R91 S95 S96 Y99 Q100
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.4.9: dTMP kinase.
Gene Ontology
Molecular Function
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
View graph for
Cellular Component
External links
PDB RCSB:2ccj, PDBe:2ccj, PDBj:2ccj
PDBsum2ccj
PubMed16522804
UniProtP65248|KTHY_STAAM Thymidylate kinase (Gene Name=tmk)

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