Structure of PDB 4hdc Chain A Binding Site BS01

Receptor Information
>4hdc Chain A (length=195) 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
EKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI
Ligand information
Ligand ID13Y
InChIInChI=1S/C28H32ClN3O5/c1-17(2)12-24(31-11-5-7-21(16-31)32-15-18(3)26(33)30-28(32)36)19-9-10-23(27(34)35)25(13-19)37-22-8-4-6-20(29)14-22/h4,6,8-10,13-15,17,21,24H,5,7,11-12,16H2,1-3H3,(H,34,35)(H,30,33,36)/t21-,24+/m0/s1
InChIKeyDUMBOKZAFBZKLT-XUZZJYLKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)C[CH](N1CCC[CH](C1)N2C=C(C)C(=O)NC2=O)c3ccc(C(O)=O)c(Oc4cccc(Cl)c4)c3
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2CCCN(C2)[C@H](CC(C)C)c3ccc(c(c3)Oc4cccc(c4)Cl)C(=O)O
CACTVS 3.370CC(C)C[C@@H](N1CCC[C@@H](C1)N2C=C(C)C(=O)NC2=O)c3ccc(C(O)=O)c(Oc4cccc(Cl)c4)c3
ACDLabs 12.01O=C(O)c2ccc(cc2Oc1cccc(Cl)c1)C(N4CCCC(N3C=C(C(=O)NC3=O)C)C4)CC(C)C
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CCCN(C2)C(CC(C)C)c3ccc(c(c3)Oc4cccc(c4)Cl)C(=O)O
FormulaC28 H32 Cl N3 O5
Name2-(3-chlorophenoxy)-4-{(1R)-3-methyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}benzoic acid
ChEMBLCHEMBL2179275
DrugBank
ZINCZINC000095572257
PDB chain4hdc 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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PDB4hdc Discovery of Selective and Potent Inhibitors of Gram-Positive Bacterial Thymidylate Kinase (TMK).
Resolution2.05 Å
Binding residue
(original residue number in PDB)		E37 R48 L52 F66 S69 R70 R92 S97 Y100 Q101
Binding residue
(residue number reindexed from 1)		E36 R47 L51 F65 S68 R69 R91 S96 Y99 Q100
Annotation score1
Binding affinityMOAD: ic50=1.2nM
PDBbind-CN: -logKd/Ki=8.92,IC50=1.2nM
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:4hdc, PDBe:4hdc, PDBj:4hdc
PDBsum4hdc
PubMed23043329
UniProtP65249|KTHY_STAAN Thymidylate kinase (Gene Name=tmk)

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