Structure of PDB 5ypi Chain E Binding Site BS01

Receptor Information

>5ypi Chain E (length=228) Species: 562 (Escherichia coli)

DQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTA
WTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYAN
ALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSD
NITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPK
ASMIVMSHSAPDSRAAITHTARMADKLR

Ligand information

• Ligand ID: 8YF
• InChI: InChI=1S/C12H19N3O5S/c1-6(16)9(11(17)18)7-4-8(10(15-7)12(19)20)21-3-2-14-5-13/h5-7,9,15-16H,2-4H2,1H3,(H2,13,14)(H,17,18)(H,19,20)/t6-,7-,9-/m1/s1
• InChIKey: KSLAOLVLEKIZMQ-ZXFLCMHBSA-N
• SMILES:
  CACTVS 3.385: C[CH](O)[CH]([CH]1CC(=C(N1)C(O)=O)SCCNC=N)C(O)=O
  CACTVS 3.385: C[C@@H](O)[C@H]([C@H]1CC(=C(N1)C(O)=O)SCCNC=N)C(O)=O
  OpenEye OEToolkits 2.0.6: [H]/N=C/NCCSC1=C(N[C@H](C1)[C@@H]([C@@H](C)O)C(=O)O)C(=O)O
  OpenEye OEToolkits 2.0.6: CC(C(C1CC(=C(N1)C(=O)O)SCCNC=N)C(=O)O)O
• Formula: C12 H19 N3 O5 S
• Name: (2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole -5-carboxylic acid;
  Imipenem, hydrolyzed form
• PDB chain: 5ypi Chain A Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ypi The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): G69 F70
• Binding residue (residue number reindexed from 1): G27 F28
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H120 H122 D124 H189 C208 K211 N220 H250
• Catalytic site (residue number reindexed from 1): H78 H80 D82 H147 C166 K169 N178 H208
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

Gene Ontology

Molecular Function

• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0017001 antibiotic catabolic process

External links

• PDB: RCSB:5ypi, PDBe:5ypi, PDBj:5ypi
• PDBsum: 5ypi
• PubMed: 29269938
• UniProt: E5KIY2