Structure of PDB 5ypm Chain F Binding Site BS03

Receptor Information
>5ypm Chain F (length=228) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTA
WTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYAN
ALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSD
NITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPK
ASMIVMSHSAPDSRAAITHTARMADKLR
Ligand information
Ligand ID8YL
InChIInChI=1S/C17H27N3O6S/c1-7-12(11(8(2)21)16(23)24)19-13(17(25)26)14(7)27-9-5-10(18-6-9)15(22)20(3)4/h7-12,18-19,21H,5-6H2,1-4H3,(H,23,24)(H,25,26)/t7-,8-,9+,10+,11-,12-/m1/s1
InChIKeyILVWWUFTACAPIZ-PQTSNVLCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](O)[CH]([CH]1NC(=C(S[CH]2CN[CH](C2)C(=O)N(C)C)[CH]1C)C(O)=O)C(O)=O
OpenEye OEToolkits 2.0.6C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)N(C)C)C(=O)O)[C@@H]([C@@H](C)O)C(=O)O
OpenEye OEToolkits 2.0.6CC1C(NC(=C1SC2CC(NC2)C(=O)N(C)C)C(=O)O)C(C(C)O)C(=O)O
CACTVS 3.385C[C@@H](O)[C@H]([C@@H]1NC(=C(S[C@@H]2CN[C@@H](C2)C(=O)N(C)C)[C@@H]1C)C(O)=O)C(O)=O
FormulaC17 H27 N3 O6 S
Name(2S,3R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfan yl-3-methyl-2,3-dihydro-1H-pyrrole-5-carboxylic acid;
Meropenem, hydrolyzed form
ChEMBL
DrugBank
ZINC
PDB chain5ypm Chain F 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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PDB5ypm The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		H122 D124 H189 C208 N220 H250
Binding residue
(residue number reindexed from 1)		H80 D82 H147 C166 N178 H208
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ypm, PDBe:5ypm, PDBj:5ypm
PDBsum5ypm
PubMed29269938
UniProtE5KIY2

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