Structure of PDB 8gpe Chain B Binding Site BS04

Receptor Information
>8gpe Chain B (length=240) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIV
RDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMD
ALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPL
KVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYA
ASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR
Ligand information
Ligand IDPNK
InChIInChI=1S/C16H20N2O5S/c1-16(2)12(15(22)23)18-13(24-16)11(14(20)21)17-10(19)8-9-6-4-3-5-7-9/h3-7,11-13,18H,8H2,1-2H3,(H,17,19)(H,20,21)(H,22,23)/t11-,12-,13+/m0/s1
InChIKeyHCYWNSXLUZRKJX-RWMBFGLXSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)Cc2ccccc2)C(O)=O
CACTVS 3.341CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)Cc2ccccc2)C(O)=O
OpenEye OEToolkits 1.5.0CC1(C(NC(S1)C(C(=O)O)NC(=O)Cc2ccccc2)C(=O)O)C
OpenEye OEToolkits 1.5.0CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)Cc2ccccc2)C(=O)O)C
ACDLabs 10.04O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)Cc2ccccc2
FormulaC16 H20 N2 O5 S
Name(2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid;
Penicillin, hydroxylated form
ChEMBLCHEMBL1235368
DrugBank
ZINCZINC000004576930
PDB chain8gpe Chain B Residue 303 [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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PDB8gpe Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed penicillin G
Resolution1.4 Å
Binding residue
(original residue number in PDB)		L65 M67 W93 H122 Q123 D124 H189 C208 K211 N220 H250
Binding residue
(residue number reindexed from 1)		L35 M37 W63 H92 Q93 D94 H159 C178 K181 N190 H220
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0017001 antibiotic catabolic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:8gpe, PDBe:8gpe, PDBj:8gpe
PDBsum8gpe
PubMed38336327
UniProtE9NWK5

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