Structure of PDB 8gpc Chain B Binding Site BS04

Receptor Information
>8gpc 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 IDZZ7
InChIInChI=1S/C16H21N3O5S/c1-16(2)11(15(23)24)19-13(25-16)10(14(21)22)18-12(20)9(17)8-6-4-3-5-7-8/h3-7,9-11,13,19H,17H2,1-2H3,(H,18,20)(H,21,22)(H,23,24)/t9-,10+,11+,13-/m1/s1
InChIKeyKDAWOPKDXRJNHV-MPPDQPJWSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)[C@H](N)c2ccccc2)C(O)=O
ACDLabs 10.04O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)C(c2ccccc2)N
OpenEye OEToolkits 1.6.1CC1(C(NC(S1)C(C(=O)O)NC(=O)C(c2ccccc2)N)C(=O)O)C
OpenEye OEToolkits 1.6.1CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)[C@@H](c2ccccc2)N)C(=O)O)C
CACTVS 3.352CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)[CH](N)c2ccccc2)C(O)=O
FormulaC16 H21 N3 O5 S
Name(2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid;
AMPICILLIN (open form)
ChEMBLCHEMBL1237008
DrugBank
ZINCZINC000034064298
PDB chain8gpc 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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PDB8gpc Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed ampicillin
Resolution1.4 Å
Binding residue
(original residue number in PDB)		M67 W93 H122 Q123 D124 H189 C208 K211 G219 N220 H250
Binding residue
(residue number reindexed from 1)		M37 W63 H92 Q93 D94 H159 C178 K181 G189 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:8gpc, PDBe:8gpc, PDBj:8gpc
PDBsum8gpc
PubMed38336327
UniProtE9NWK5

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