Structure of PDB 4de2 Chain A Binding Site BS01

Receptor Information
>4de2 Chain A (length=260) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAA
AVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQ
YSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPR
DTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTS
WTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLA
SAARIIAEGL
Ligand information
Ligand IDDN3
InChIInChI=1S/C17H18N6O/c1-23(2)11-12-5-3-7-14(9-12)17(24)18-15-8-4-6-13(10-15)16-19-21-22-20-16/h3-10H,11H2,1-2H3,(H,18,24)(H,19,20,21,22)
InChIKeyYNFKRUNLXWQDEZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370
OpenEye OEToolkits 1.7.6		CN(C)Cc1cccc(c1)C(=O)Nc2cccc(c2)c3[nH]nnn3
ACDLabs 12.01O=C(c1cccc(c1)CN(C)C)Nc2cccc(c2)c3nnnn3
FormulaC17 H18 N6 O
Name3-[(dimethylamino)methyl]-N-[3-(1H-tetrazol-5-yl)phenyl]benzamide
ChEMBLCHEMBL2031553
DrugBank
ZINC
PDB chain4de2 Chain A Residue 301 [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]
PDB4de2 Structure-Based Design of Potent and Ligand-Efficient Inhibitors of CTX-M Class A Beta-Lactamase
Resolution1.4 Å
Binding residue
(original residue number in PDB)		N104 Y105 S130 N132 P167 N170 T235 G236 S237 D240
Binding residue
(residue number reindexed from 1)		N76 Y77 S102 N104 P139 N142 T207 G208 S209 D211
Annotation score1
Binding affinityMOAD: Ki=76uM
PDBbind-CN: -logKd/Ki=4.12,Ki=76.0uM
Enzymatic activity
Catalytic site (original residue number in PDB) S70 K73 S130 E166 K234 S237
Catalytic site (residue number reindexed from 1) S42 K45 S102 E138 K206 S209
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:0030655 beta-lactam antibiotic catabolic process
GO:0046677 response to antibiotic

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4de2, PDBe:4de2, PDBj:4de2
PDBsum4de2
PubMed22296601
UniProtQ9L5C8

[Back to BioLiP]