Structure of PDB 5ypk Chain D Binding Site BS03

Receptor Information
>5ypk Chain D (length=229) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDT
AWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYA
NALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTS
DNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFP
KASMIVMSHSAPDSRAAITHTARMADKLR
Ligand information
Ligand IDHIW
InChIInChI=1S/C12H19N3O5S/c1-6(16)9(11(17)18)7-4-8(10(15-7)12(19)20)21-3-2-14-5-13/h5-9,16H,2-4H2,1H3,(H2,13,14)(H,17,18)(H,19,20)/t6-,7-,8+,9-/m1/s1
InChIKeyGGEWNUMDSNUHAH-LURQLKTLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4[H]/N=C\NCCS[C@H]1C[C@@H](N=C1C(=O)O)[C@@H]([C@@H](C)O)C(=O)O
OpenEye OEToolkits 2.0.4CC(C(C1CC(C(=N1)C(=O)O)SCCNC=N)C(=O)O)O
CACTVS 3.385C[C@@H](O)[C@H]([C@H]1C[C@H](SCCNC=N)C(=N1)C(O)=O)C(O)=O
CACTVS 3.385C[CH](O)[CH]([CH]1C[CH](SCCNC=N)C(=N1)C(O)=O)C(O)=O
ACDLabs 12.01O=C(O)C1=NC(CC1SCCN[C@H]=N)C(C(O)=O)C(O)C
FormulaC12 H19 N3 O5 S
Name(2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid;
Hydrolyzed Imipenem
ChEMBL
DrugBank
ZINCZINC000139534184
PDB chain5ypk Chain D Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ypk The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		W93 H122 D124 H189 K211 G219 N220 H250
Binding residue
(residue number reindexed from 1)		W52 H81 D83 H148 K170 G178 N179 H209
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) H79 H81 D83 H148 C167 K170 N179 H209
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:5ypk, PDBe:5ypk, PDBj:5ypk
PDBsum5ypk
PubMed29269938
UniProtE5KIY2

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