Structure of PDB 8vbw Chain A Binding Site BS01

Receptor Information
>8vbw Chain A (length=505) Species: 2043664 (Staphylococcaceae bacterium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QQPERGKIYDRNGKVLAEDVERYKLVAVIDKKASANSKKPRHVVDKKETA
KKLSTVIDMKPEEIEKRLSQKKAFQIEFGRKGTNLTYQDKLKIEKMNLPG
ISLLPETERFYPNGNFASHLIGRAQKNPDTGELKGALGVEKIFDSYLSGK
RGDDVHLTIDSNIQVFVEEALDGMVERYQPKDLFAVVMDAKTGEILAYSQ
RPTFNPETGKDFGKKWANDLYQNTYEPGSTFKSYGLAAAIQEGAFDPDKK
YKSGHRDIMGSRISDWNRVGWGEIPMSLGFTYSSNTLMMHLQDLVGADKM
KSWYERFGFGKSTKGMFDGEAPGQIGWSNELQQKTSSFGQSTTVTPVQML
QAQSAFFNDGNMLKPWFVNSVENPVSKRQFYKGQKQIAGKPITKDTAEKV
EKQLDLVVNSKKSHAANYRIDGYEVEGKTGTAQVAAPNGGGYVKGPNPYF
VSFMGDAPKKNPKVIVYAGMSLAQKNDQEAYELGVSKAFKPIMENTLKYL
NVGKS
Ligand information
Ligand ID1RG
InChIInChI=1S/C22H27N3O7S/c1-10-17(15(9-26)11(2)27)25-18(22(31)32)19(10)33-14-7-16(23-8-14)20(28)24-13-5-3-4-12(6-13)21(29)30/h3-6,9-11,14-17,23,25,27H,7-8H2,1-2H3,(H,24,28)(H,29,30)(H,31,32)/t10-,11-,14+,15-,16+,17-/m1/s1
InChIKeyPGRRQYXTRXQDDJ-SKHPLXCOSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)c1cc(ccc1)NC(=O)C3NCC(SC2=C(C(=O)O)NC(C2C)C(C=O)C(O)C)C3
OpenEye OEToolkits 1.7.6C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)Nc3cccc(c3)C(=O)O)C(=O)O)[C@H](C=O)[C@@H](C)O
OpenEye OEToolkits 1.7.6CC1C(NC(=C1SC2CC(NC2)C(=O)Nc3cccc(c3)C(=O)O)C(=O)O)C(C=O)C(C)O
CACTVS 3.370C[CH](O)[CH](C=O)[CH]1NC(=C(S[CH]2CN[CH](C2)C(=O)Nc3cccc(c3)C(O)=O)[CH]1C)C(O)=O
CACTVS 3.370C[C@@H](O)[C@@H](C=O)[C@@H]1NC(=C(S[C@@H]2CN[C@@H](C2)C(=O)Nc3cccc(c3)C(O)=O)[C@@H]1C)C(O)=O
FormulaC22 H27 N3 O7 S
Name(4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid;
ERTAPENEM, bound form PRE-ISOMERIZED
ChEMBL
DrugBank
ZINCZINC000103522323
PDB chain8vbw Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8vbw Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1.
Resolution2.3 Å
Binding residue
(original residue number in PDB)
S314 W351 S368 N370 H499 T514 G515 T516 Y566 E567
Binding residue
(residue number reindexed from 1)
S229 W266 S283 N285 H414 T429 G430 T431 Y481 E482
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008658 penicillin binding

View graph for
Molecular Function
External links
PDB RCSB:8vbw, PDBe:8vbw, PDBj:8vbw
PDBsum8vbw
PubMed38527711
UniProtQ2FZ94

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