Structure of PDB 4cfe Chain D Binding Site BS01

Receptor Information
>4cfe Chain D (length=167) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RPTVFRWTGGGKEVYLSGSFNNWSKLPLTRSHNNFVAILDLPEGEHQYKF
FVDGQWTHDPSEPIVTSQLGTVNNIIQVKKTDFEVFDALMVDSQEPYVCP
PILPPHLLQVILNKDTGISCDPALLPEPNHVMLNHLYALSIKDGVMVLSA
THRYKKKYVTTLLYKPI
Ligand information
Ligand ID992
InChIInChI=1S/C24H18ClN3O3/c1-13-3-5-16(10-17(13)23(29)30)31-24-26-20-11-18(19(25)12-21(20)27-24)14-4-6-22-15(9-14)7-8-28(22)2/h3-12H,1-2H3,(H,26,27)(H,29,30)
InChIKeyFHWSAZXFPUMKFL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)c5cc(Oc4nc3cc(c1cc2c(cc1)n(cc2)C)c(Cl)cc3n4)ccc5C
OpenEye OEToolkits 1.9.2Cc1ccc(cc1C(=O)O)Oc2[nH]c3cc(c(cc3n2)c4ccc5c(c4)ccn5C)Cl
CACTVS 3.385Cn1ccc2cc(ccc12)c3cc4nc([nH]c4cc3Cl)Oc5ccc(C)c(c5)C(O)=O
FormulaC24 H18 Cl N3 O3
Name5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic acid
ChEMBLCHEMBL3393127
DrugBank
ZINCZINC000095921139
PDB chain4cfe Chain C Residue 1553 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4cfe Structural Basis of Ampk Regulation by Small Molecule Activators.
Resolution3.023 Å
Binding residue
(original residue number in PDB)		R83 R107 S108 N111 V113
Binding residue
(residue number reindexed from 1)		R6 R30 S31 N34 V36
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.22,Kd=0.06uM
BindingDB: EC50=2.0nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0005515 protein binding
GO:0019901 protein kinase binding
Biological Process
GO:0006468 protein phosphorylation
GO:0006633 fatty acid biosynthetic process
GO:0007165 signal transduction
GO:0010628 positive regulation of gene expression
GO:0031669 cellular response to nutrient levels
GO:0035878 nail development
GO:0120162 positive regulation of cold-induced thermogenesis
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0031588 nucleotide-activated protein kinase complex
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4cfe, PDBe:4cfe, PDBj:4cfe
PDBsum4cfe
PubMed24352254
UniProtQ9Y478|AAKB1_HUMAN 5'-AMP-activated protein kinase subunit beta-1 (Gene Name=PRKAB1)

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