Structure of PDB 6f2n Chain A Binding Site BS03

Receptor Information
>6f2n Chain A (length=219) Species: 1396 (Bacillus cereus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKTVIKNETGTISISQLNKNVWVHTELGSAVPSNGLVLNTSKGLVLVDSS
WDDKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGIKTLKERGIKAHST
ALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWL
PQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVP
GHGEVGDKGLLLHTLDLLK
Ligand information
Ligand IDCF8
InChIInChI=1S/C20H16O2S/c21-20(22)19(23)13-18-8-4-3-7-17(18)12-14-9-10-15-5-1-2-6-16(15)11-14/h1-11,13,23H,12H2,(H,21,22)/b19-13-
InChIKeyLALSQKFPBIDRFB-UYRXBGFRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc2cc(ccc2c1)Cc3ccccc3C=C(C(=O)O)S
CACTVS 3.385OC(=O)C(S)=Cc1ccccc1Cc2ccc3ccccc3c2
OpenEye OEToolkits 2.0.6c1ccc2cc(ccc2c1)Cc3ccccc3/C=C(/C(=O)O)\S
CACTVS 3.385OC(=O)/C(S)=C/c1ccccc1Cc2ccc3ccccc3c2
FormulaC20 H16 O2 S
Name(~{Z})-3-[2-(naphthalen-2-ylmethyl)phenyl]-2-sulfanyl-prop-2-enoic acid
ChEMBLCHEMBL4128221
DrugBank
ZINC
PDB chain6f2n Chain A Residue 304 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6f2n Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-beta-lactamases.
Resolution1.149 Å
Binding residue
(original residue number in PDB)		V69 H118 D120 H179 C198 N210 H240
Binding residue
(residue number reindexed from 1)		V31 H80 D82 H141 C160 N172 H202
Annotation score1
Binding affinityMOAD: ic50=0.2uM
PDBbind-CN: -logKd/Ki=6.70,IC50=0.2uM
BindingDB: IC50=200nM
Enzymatic activity
Catalytic site (original residue number in PDB) H116 H118 D120 H179 C198 K201 N210 H240
Catalytic site (residue number reindexed from 1) H78 H80 D82 H141 C160 K163 N172 H202
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6f2n, PDBe:6f2n, PDBj:6f2n
PDBsum6f2n
PubMed29655609
UniProtP04190|BLA2_BACCE Metallo-beta-lactamase type 2 (Gene Name=blm)

[Back to BioLiP]