Structure of PDB 8i8f Chain B Binding Site BS04

Receptor Information

>8i8f Chain B (length=239) Species: 573 (Klebsiella pneumoniae)

RPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVR
DGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDA
LHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLK
VFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAA
SARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR

Ligand information

• Ligand ID: OL6
• InChI: InChI=1S/C20H22N2O6S/c1-20(2)16(19(26)27)22-17(29-20)15(18(24)25)21-14(23)10-28-13-9-5-7-11-6-3-4-8-12(11)13/h3-9,15-17,22H,10H2,1-2H3,(H,21,23)(H,24,25)(H,26,27)/t15-,16-,17+/m0/s1
• InChIKey: UGGIHYYCRXQWCH-YESZJQIVSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC1(C(NC(S1)C(C(=O)O)NC(=O)COc2cccc3c2cccc3)C(=O)O)C
  CACTVS 3.385: CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)COc2cccc3ccccc23)C(O)=O
  CACTVS 3.385: CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)COc2cccc3ccccc23)C(O)=O
  OpenEye OEToolkits 2.0.7: CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)COc2cccc3c2cccc3)C(=O)O)C
• Formula: C20 H22 N2 O6 S
• Name: (2R,4S)-5,5-dimethyl-2-[(1R)-1-(2-naphthalen-1-yloxyethanoylamino)-2-oxidanyl-2-oxidanylidene-ethyl]-1,3-thiazolidine-4-carboxylic acid
• PDB chain: 8i8f Chain B Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8i8f Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed compound 1
• Resolution: 1.89 Å
• Binding residue (original residue number in PDB): V73 W93 H122 Q123 D124 H189 C208 K211 G219 N220 H250
• Binding residue (residue number reindexed from 1): V42 W62 H91 Q92 D93 H158 C177 K180 G188 N189 H219
• 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:8i8f, PDBe:8i8f, PDBj:8i8f
• PDBsum: 8i8f
• PubMed: 38336327
• UniProt: E9NWK5