Structure of PDB 4qgh Chain B Binding Site BS01

Receptor Information
>4qgh Chain B (length=198) 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
GYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKRLDQEDL
KFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI
Ligand information
Ligand ID32E
InChIInChI=1S/C28H31ClFN3O5/c1-16(2)12-23(32-11-5-7-19(15-32)33-14-17(3)26(34)31-28(33)37)21-9-10-22(27(35)36)25(24(21)30)38-20-8-4-6-18(29)13-20/h4,6,8-10,13-14,16,19,23H,5,7,11-12,15H2,1-3H3,(H,35,36)(H,31,34,37)/t19-,23-/m0/s1
InChIKeyIYCZAWHAUDFBFO-CVDCTZTESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2CCCN(C2)[C@@H](CC(C)C)c3ccc(c(c3F)Oc4cccc(c4)Cl)C(=O)O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CCCN(C2)C(CC(C)C)c3ccc(c(c3F)Oc4cccc(c4)Cl)C(=O)O
CACTVS 3.385CC(C)C[CH](N1CCC[CH](C1)N2C=C(C)C(=O)NC2=O)c3ccc(C(O)=O)c(Oc4cccc(Cl)c4)c3F
CACTVS 3.385CC(C)C[C@H](N1CCC[C@@H](C1)N2C=C(C)C(=O)NC2=O)c3ccc(C(O)=O)c(Oc4cccc(Cl)c4)c3F
ACDLabs 12.01O=C(O)c2ccc(c(F)c2Oc1cccc(Cl)c1)C(N4CCCC(N3C=C(C(=O)NC3=O)C)C4)CC(C)C
FormulaC28 H31 Cl F N3 O5
Name2-(3-chlorophenoxy)-3-fluoro-4-{(1S)-3-methyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}benzoic acid
ChEMBLCHEMBL3298206
DrugBank
ZINCZINC000098208384
PDB chain4qgh Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4qgh Antibacterial inhibitors of gram-positive thymidylate kinase: structure-activity relationships and chiral preference of a new hydrophobic binding region.
Resolution1.78 Å
Binding residue
(original residue number in PDB)		E37 R48 L52 F66 R70 R92 S96 S97 Y100 Q101
Binding residue
(residue number reindexed from 1)		E36 R47 L51 F65 R69 R91 S95 S96 Y99 Q100
Annotation score1
Binding affinityMOAD: ic50=1nM
PDBbind-CN: -logKd/Ki=9.00,IC50=1nM
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:4qgh, PDBe:4qgh, PDBj:4qgh
PDBsum4qgh
PubMed24828090
UniProtQ6GJI9|KTHY_STAAR Thymidylate kinase (Gene Name=tmk)

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