Structure of PDB 6zyq Chain B Binding Site BS03

Receptor Information
>6zyq Chain B (length=228) Species: 573 (Klebsiella pneumoniae) [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 IDQST
InChIInChI=1S/C10H17NO4S2/c1-4-15-8(14)10(5-16)11-6(7(12)13)9(2,3)17-10/h6,11,16H,4-5H2,1-3H3,(H,12,13)/t6-,10+/m0/s1
InChIKeyPUOMKKVEJFJZFE-QUBYGPBYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCOC(=O)C1(NC(C(S1)(C)C)C(=O)O)CS
CACTVS 3.385CCOC(=O)[C@]1(CS)N[C@@H](C(O)=O)C(C)(C)S1
OpenEye OEToolkits 2.0.7CCOC(=O)[C@@]1(N[C@H](C(S1)(C)C)C(=O)O)CS
CACTVS 3.385CCOC(=O)[C]1(CS)N[CH](C(O)=O)C(C)(C)S1
FormulaC10 H17 N O4 S2
Name(2~{S},4~{S})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6zyq Chain B Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6zyq 2-Mercaptomethyl-thiazolidines use conserved aromatic-S interactions to achieve broad-range inhibition of metallo-beta-lactamases.
Resolution1.7 Å
Binding residue
(original residue number in PDB)
W93 H122 D124 H189 G219 N220 H250
Binding residue
(residue number reindexed from 1)
W51 H80 D82 H147 G177 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:0008270 zinc ion binding
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0017001 antibiotic catabolic process
GO:0046677 response to antibiotic
Cellular Component
GO:0042597 periplasmic space

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:6zyq, PDBe:6zyq, PDBj:6zyq
PDBsum6zyq
PubMed34164056
UniProtC7C422|BLAN1_KLEPN Metallo-beta-lactamase type 2 (Gene Name=blaNDM-1)

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