Structure of PDB 5ty7 Chain B Binding Site BS01

Receptor Information
>5ty7 Chain B (length=358) Species: 93062 (Staphylococcus aureus subsp. aureus COL) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TNSDVTPVQAANQYGYAGLSAAYEPTSAVNVSQTGQLLYQYNIDTKWNPA
SMTKLMTMYLTLEAVNKGQLSLDDTVTMTNKEYIMSTLPELSNTKLYPGQ
VWTIADLLQITVSNSSNAAALILAKKVSKNTSDFVDLMNNKAKAIGMKNT
HFVNPTGAENSRLRTFAPTKYKDQERTVTTARDYAILDLHVIKETPKILD
FTKQLAPTTHAVTYYTFNFSLEGAKMSLPGTDGLKTGSSDTANYNHTITT
KRGKFRINQVIMGAGDYKNLGGEKQRNMMGNALMERSFDQYKYVKILSKG
EQRINGKKYYVENDLYDVLPSDFSKKDYKLVVEDGKVHADYPREFINKDY
GPPTVEVH
Ligand information
Ligand IDNFF
InChIInChI=1S/C21H24N2O5S/c1-4-28-15-10-9-12-7-5-6-8-13(12)16(15)18(25)22-14(11-24)19-23-17(20(26)27)21(2,3)29-19/h5-11,14,17,19,23H,4H2,1-3H3,(H,22,25)(H,26,27)/t14-,17+,19-/m1/s1
InChIKeyXDLYHUOUOKHAMD-DKSSEZFCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCOc1ccc2ccccc2c1C(=O)NC(C=O)C3NC(C(S3)(C)C)C(=O)O
ACDLabs 12.01O=C(NC(C=O)C1SC(C(N1)C(=O)O)(C)C)c3c2ccccc2ccc3OCC
OpenEye OEToolkits 1.7.6CCOc1ccc2ccccc2c1C(=O)N[C@H](C=O)[C@@H]3N[C@H](C(S3)(C)C)C(=O)O
CACTVS 3.370CCOc1ccc2ccccc2c1C(=O)N[CH](C=O)[CH]3N[CH](C(O)=O)C(C)(C)S3
CACTVS 3.370CCOc1ccc2ccccc2c1C(=O)N[C@H](C=O)[C@@H]3N[C@@H](C(O)=O)C(C)(C)S3
FormulaC21 H24 N2 O5 S
Name(2R,4S)-2-[(1R)-1-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid;
Nafcillin, bound form
ChEMBL
DrugBank
ZINCZINC000095921260
PDB chain5ty7 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5ty7 Structural and kinetic analysis of penicillin-binding protein 4 (PBP4)-mediated antibiotic resistance inStaphylococcus aureus.
Resolution1.894 Å
Binding residue
(original residue number in PDB)		S75 S116 S139 T260 G261 S262 Y291
Binding residue
(residue number reindexed from 1)		S51 S92 S115 T236 G237 S238 Y267
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004180 carboxypeptidase activity
GO:0008800 beta-lactamase activity
GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity
Biological Process
GO:0006508 proteolysis
GO:0030655 beta-lactam antibiotic catabolic process
GO:0046677 response to antibiotic

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ty7, PDBe:5ty7, PDBj:5ty7
PDBsum5ty7
PubMed30366985
UniProtA0A0H2WY27

[Back to BioLiP]