Structure of PDB 4gfd Chain B Binding Site BS01

Receptor Information
>4gfd Chain B (length=193) 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
LEGDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQG
YARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIDQEDLKFHEK
VIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI
Ligand information
Ligand ID0YB
InChIInChI=1S/C29H34BrN3O5/c1-18-16-33(28(37)31-26(18)34)21-8-6-12-32(17-21)24(15-29(2,3)4)19-10-11-23(27(35)36)25(13-19)38-22-9-5-7-20(30)14-22/h5,7,9-11,13-14,16,21,24H,6,8,12,15,17H2,1-4H3,(H,35,36)(H,31,34,37)/t21-,24+/m0/s1
InChIKeySXYGLXXKMZTVNB-XUZZJYLKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2CCCN(C2)[C@H](CC(C)(C)C)c3ccc(c(c3)Oc4cccc(c4)Br)C(=O)O
CACTVS 3.370CC1=CN([C@H]2CCCN(C2)[C@H](CC(C)(C)C)c3ccc(C(O)=O)c(Oc4cccc(Br)c4)c3)C(=O)NC1=O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CCCN(C2)C(CC(C)(C)C)c3ccc(c(c3)Oc4cccc(c4)Br)C(=O)O
ACDLabs 12.01O=C(O)c2ccc(cc2Oc1cccc(Br)c1)C(N4CCCC(N3C=C(C(=O)NC3=O)C)C4)CC(C)(C)C
CACTVS 3.370CC1=CN([CH]2CCCN(C2)[CH](CC(C)(C)C)c3ccc(C(O)=O)c(Oc4cccc(Br)c4)c3)C(=O)NC1=O
FormulaC29 H34 Br N3 O5
Name2-(3-bromophenoxy)-4-{(1R)-3,3-dimethyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}benzoic acid
ChEMBLCHEMBL2179277
DrugBank
ZINC
PDB chain4gfd 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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PDB4gfd In Vivo Validation of Thymidylate Kinase (TMK) with a Rationally Designed, Selective Antibacterial Compound.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		E37 R48 L52 F66 S69 R70 R92 S96 S97 Y100 Q101
Binding residue
(residue number reindexed from 1)		E36 R47 L51 F64 S67 R68 R90 S94 S95 Y98 Q99
Annotation score1
Binding affinityMOAD: Ki=330pM
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:4gfd, PDBe:4gfd, PDBj:4gfd
PDBsum4gfd
PubMed22908966
UniProtP65248|KTHY_STAAM Thymidylate kinase (Gene Name=tmk)

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