Structure of PDB 4gsy Chain A Binding Site BS01

Receptor Information
>4gsy Chain A (length=191) Species: 158879 (Staphylococcus aureus subsp. aureus N315) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIV
LEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQ
GYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIDQEDLKFH
EKVIEGYQEIIHQRFKSVNADQPLENVVEDTYQTIIKYLEK
Ligand information
Ligand ID0Y5
InChIInChI=1S/C25H24F3N3O5/c1-15-12-31(24(35)29-22(15)32)18-5-3-9-30(14-18)13-16-7-8-20(23(33)34)21(10-16)36-19-6-2-4-17(11-19)25(26,27)28/h2,4,6-8,10-12,18H,3,5,9,13-14H2,1H3,(H,33,34)(H,29,32,35)/t18-/m0/s1
InChIKeySLYIQORXPGMWOF-SFHVURJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC1=CN([C@H]2CCCN(C2)Cc3ccc(C(O)=O)c(Oc4cccc(c4)C(F)(F)F)c3)C(=O)NC1=O
ACDLabs 12.01FC(F)(F)c4cc(Oc1cc(ccc1C(=O)O)CN3CCCC(N2C=C(C(=O)NC2=O)C)C3)ccc4
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CCCN(C2)Cc3ccc(c(c3)Oc4cccc(c4)C(F)(F)F)C(=O)O
CACTVS 3.370CC1=CN([CH]2CCCN(C2)Cc3ccc(C(O)=O)c(Oc4cccc(c4)C(F)(F)F)c3)C(=O)NC1=O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2CCCN(C2)Cc3ccc(c(c3)Oc4cccc(c4)C(F)(F)F)C(=O)O
FormulaC25 H24 F3 N3 O5
Name4-{[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]methyl}-2-[3-(trifluoromethyl)phenoxy]benzoic acid
ChEMBLCHEMBL2179669
DrugBank
ZINCZINC000095578625
PDB chain4gsy Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4gsy Discovery of Selective and Potent Inhibitors of Gram-Positive Bacterial Thymidylate Kinase (TMK).
Resolution1.71 Å
Binding residue
(original residue number in PDB)		E37 R48 V51 L52 F66 S69 R70 R92 S97 Y100 Q101
Binding residue
(residue number reindexed from 1)		E36 R47 V50 L51 F65 S68 R69 R91 S96 Y99 Q100
Annotation score1
Binding affinityMOAD: ic50=120nM
PDBbind-CN: -logKd/Ki=6.92,IC50=120nM
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:4gsy, PDBe:4gsy, PDBj:4gsy
PDBsum4gsy
PubMed23043329
UniProtQ6GJI9|KTHY_STAAR Thymidylate kinase (Gene Name=tmk)

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