Structure of PDB 8gpc Chain B Binding Site BS01

Receptor Information

>8gpc Chain B (length=240) Species: 573 (Klebsiella pneumoniae)

IRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIV
RDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMD
ALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPL
KVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYA
ASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR

Ligand information

• Ligand ID: ZZ7
• InChI: InChI=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
• InChIKey: KDAWOPKDXRJNHV-MPPDQPJWSA-N
• SMILES:
  CACTVS 3.352: CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)[C@H](N)c2ccccc2)C(O)=O
  ACDLabs 10.04: O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)C(c2ccccc2)N
  OpenEye OEToolkits 1.6.1: CC1(C(NC(S1)C(C(=O)O)NC(=O)C(c2ccccc2)N)C(=O)O)C
  OpenEye OEToolkits 1.6.1: CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)[C@@H](c2ccccc2)N)C(=O)O)C
  CACTVS 3.352: CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)[CH](N)c2ccccc2)C(O)=O
• Formula: C16 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)
• ChEMBL: CHEMBL1237008
• ZINC: ZINC000034064298
• PDB chain: 8gpc Chain A Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8gpc Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed ampicillin
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): P68 G69 F70
• Binding residue (residue number reindexed from 1): P38 G39 F40
• Annotation score: 1

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

External links

• PDB: RCSB:8gpc, PDBe:8gpc, PDBj:8gpc
• PDBsum: 8gpc
• PubMed: 38336327
• UniProt: E9NWK5