Structure of PDB 3bm6 Chain B Binding Site BS01

Receptor Information
>3bm6 Chain B (length=358) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQP
VTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNG
ITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANS
SIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPAEEKNYAWGY
REGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQ
LAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSDNKIALAARPVKAITP
PTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVDAA
WQILNALQ
Ligand information
Ligand IDC9P
InChIInChI=1S/C17H14BNO8S3/c20-17(21)14-7-6-11(18(22)23)8-15(14)19-30(26,27)16-9-13(10-28-16)29(24,25)12-4-2-1-3-5-12/h1-10,19,22-23H,(H,20,21)
InChIKeyJJPKFZAOXOEFHQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0B(c1ccc(c(c1)NS(=O)(=O)c2cc(cs2)S(=O)(=O)c3ccccc3)C(=O)O)(O)O
CACTVS 3.341OB(O)c1ccc(C(O)=O)c(N[S](=O)(=O)c2scc(c2)[S](=O)(=O)c3ccccc3)c1
ACDLabs 10.04O=S(=O)(c1csc(c1)S(=O)(=O)Nc2cc(B(O)O)ccc2C(=O)O)c3ccccc3
FormulaC17 H14 B N O8 S3
Name4-(dihydroxyboranyl)-2-({[4-(phenylsulfonyl)thiophen-2-yl]sulfonyl}amino)benzoic acid;
3-(4-BENZENESULFONYL-THIOPHENE-2-SULFONYLAMINO)-4-CARBOXY-PHENYLBORONIC ACID
ChEMBLCHEMBL1084081
DrugBankDB07541
ZINCZINC000169748499
PDB chain3bm6 Chain B Residue 2 [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]
PDB3bm6 Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		S64 Q120 Y150 N152 Y221 G317 A318 T319
Binding residue
(residue number reindexed from 1)		S61 Q117 Y147 N149 Y218 G314 A315 T316
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S64 K67 Y112 A114 V121 Y150 G156 E272 K315 A318
Catalytic site (residue number reindexed from 1) S61 K64 Y109 A111 V118 Y147 G153 E269 K312 A315
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:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3bm6, PDBe:3bm6, PDBj:3bm6
PDBsum3bm6
PubMed20452208
UniProtP00811|AMPC_ECOLI Beta-lactamase (Gene Name=ampC)

[Back to BioLiP]