Structure of PDB 8gpd Chain A Binding Site BS03

Receptor Information

>8gpd Chain A (length=240) Species: 573 (Klebsiella pneumoniae)

IRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIV
RDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMD
ALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPL
KVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYA
ASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR

Ligand information

• Ligand ID: JXF
• InChI: InChI=1S/C16H20N2O6S/c1-16(2)12(15(22)23)18-13(25-16)11(14(20)21)17-10(19)8-24-9-6-4-3-5-7-9/h3-7,11-13,18H,8H2,1-2H3,(H,17,19)(H,20,21)(H,22,23)/t11-,12-,13+/m0/s1
• InChIKey: FJTUHYOOCYRLJI-RWMBFGLXSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC1(C(NC(S1)C(C(=O)O)NC(=O)COc2ccccc2)C(=O)O)C
  CACTVS 3.385: CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)COc2ccccc2)C(O)=O
  OpenEye OEToolkits 2.0.7: CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)COc2ccccc2)C(=O)O)C
  CACTVS 3.385: CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)COc2ccccc2)C(O)=O
• Formula: C16 H20 N2 O6 S
• Name: (2R,4S)-5,5-dimethyl-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-phenoxyethanoylamino)ethyl]-1,3-thiazolidine-4-carboxylic acid
• ZINC: ZINC000001621018
• PDB chain: 8gpd Chain A Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8gpd Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed penicillin V
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): M67 W93 H122 Q123 D124 H189 C208 K211 N220 H250
• Binding residue (residue number reindexed from 1): M37 W63 H92 Q93 D94 H159 C178 K181 N190 H220
• 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:8gpd, PDBe:8gpd, PDBj:8gpd
• PDBsum: 8gpd
• PubMed: 38336327
• UniProt: E9NWK5