Structure of PDB 7mdc Chain A Binding Site BS02

Receptor Information
>7mdc Chain A (length=438) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IGAQDERLSTLIHQRMQEAKVPALSVSVTIKGVRQRFVYGVADVASQKAN
TLDTVYELGSMSKAFTGLVVQILIQEGRLRQGDDIITYLPEMRLNYQGKP
ASLTVADFLYHTSGLPFSTLARLENPMPGSAVAQQLRNENLLFAPGAKFS
YASANYDVLGAVIENVTGKTFTEVIAERLTQPLGMSATVAVKGDEIIVNK
ASGYKLGFGKPVLFHAPLARNHVPAAYIHSTLPDMEIWIDAWLHRKALPA
TLREAMSNSWRGNSDVPLAADNRILYASGWFIDQNQGPYISHGGQNPNFS
SCIALRPDQQIGIVALANMNSNLILQLCADIDNYLRIGKYADGAGDAITA
TDTLFVYLTLLLCFWGAVVVVRGAFRVRDYIIALAVPGLVAAMLYVAPGI
LSPGLDWRFILVWGPSSVLAIPFGIILLAFVLTLNHQI
Ligand information
Ligand IDYX7
InChIInChI=1S/C9H19BN2O4/c1-2-3-4-5-9(14)12-7(10(15)16)6-8(11)13/h7,15-16H,2-6H2,1H3,(H2,11,13)(H,12,14)/t7-/m1/s1
InChIKeyJFQHYAGISMLDGO-SSDOTTSWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCC(=O)N[CH](CC(N)=O)B(O)O
ACDLabs 12.01O=C(NC(CC(N)=O)B(O)O)CCCCC
CACTVS 3.385CCCCCC(=O)N[C@H](CC(N)=O)B(O)O
OpenEye OEToolkits 2.0.7B(C(CC(=O)N)NC(=O)CCCCC)(O)O
OpenEye OEToolkits 2.0.7B([C@@H](CC(=O)N)NC(=O)CCCCC)(O)O
FormulaC9 H19 B N2 O4
Name[(1S)-3-amino-1-(hexanoylamino)-3-oxopropyl]boronic acid
ChEMBL
DrugBank
ZINC
PDB chain7mdc Chain A Residue 609 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7mdc A small molecule inhibitor prevents gut bacterial genotoxin production.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		S95 L155 Y186 S188 H257 A261 Q330 N331 W466
Binding residue
(residue number reindexed from 1)		S60 L120 Y151 S153 H222 A226 Q295 N296 W413
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
Biological Process
GO:0017001 antibiotic catabolic process
GO:0046677 response to antibiotic
Cellular Component
GO:0016020 membrane
GO:0030288 outer membrane-bounded periplasmic space

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7mdc, PDBe:7mdc, PDBj:7mdc
PDBsum7mdc
PubMed36253549
UniProtQ0P7K6

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