Structure of PDB 4qgf Chain A Binding Site BS01

Receptor Information
>4qgf Chain A (length=196) Species: 282458 (Staphylococcus aureus subsp. aureus MRSA252) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIV
LEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQ
GYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKDQEDLKF
HEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI
Ligand information
Ligand ID32B
InChIInChI=1S/C27H30ClN3O6/c1-4-22(30-12-6-8-18(15-30)31-14-16(2)25(32)29-27(31)35)20-10-11-21(26(33)34)24(23(20)36-3)37-19-9-5-7-17(28)13-19/h5,7,9-11,13-14,18,22H,4,6,8,12,15H2,1-3H3,(H,33,34)(H,29,32,35)/t18-,22+/m0/s1
InChIKeyLWVFVEIAPUMILP-PGRDOPGGSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)c2ccc(c(OC)c2Oc1cccc(Cl)c1)C(N4CCCC(N3C=C(C(=O)NC3=O)C)C4)CC
OpenEye OEToolkits 1.7.6CCC(c1ccc(c(c1OC)Oc2cccc(c2)Cl)C(=O)O)N3CCCC(C3)N4C=C(C(=O)NC4=O)C
CACTVS 3.385CC[CH](N1CCC[CH](C1)N2C=C(C)C(=O)NC2=O)c3ccc(C(O)=O)c(Oc4cccc(Cl)c4)c3OC
OpenEye OEToolkits 1.7.6CC[C@H](c1ccc(c(c1OC)Oc2cccc(c2)Cl)C(=O)O)N3CCC[C@@H](C3)N4C=C(C(=O)NC4=O)C
CACTVS 3.385CC[C@@H](N1CCC[C@@H](C1)N2C=C(C)C(=O)NC2=O)c3ccc(C(O)=O)c(Oc4cccc(Cl)c4)c3OC
FormulaC27 H30 Cl N3 O6
Name2-(3-chlorophenoxy)-3-methoxy-4-{(1R)-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]propyl}benzoic acid
ChEMBLCHEMBL3297963
DrugBank
ZINCZINC000098208382
PDB chain4qgf 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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PDB4qgf Antibacterial inhibitors of gram-positive thymidylate kinase: structure-activity relationships and chiral preference of a new hydrophobic binding region.
Resolution1.83 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=69nM
PDBbind-CN: -logKd/Ki=7.16,IC50=69nM
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
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Cellular Component
External links
PDB RCSB:4qgf, PDBe:4qgf, PDBj:4qgf
PDBsum4qgf
PubMed24828090
UniProtQ6GJI9|KTHY_STAAR Thymidylate kinase (Gene Name=tmk)

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