Structure of PDB 6c9j Chain A Binding Site BS01

Receptor Information
>6c9j Chain A (length=386) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVV
GKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKN
GRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADF
GLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALL
CGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRAT
IKDIREHEWFKQDLPKYLFPETRPHPERVPFLVAKAKWHLGIRSQSRPND
IMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTYSKMSLQLYQVDSRT
YLLDFRSIDDELTPRPGSHTIEFFEMCANLIKILAQ
Ligand information
Ligand IDR34
InChIInChI=1S/C24H19ClN4O3/c1-13-3-5-16(10-17(13)23(30)28-31)32-24-26-20-11-18(19(25)12-21(20)27-24)14-4-6-22-15(9-14)7-8-29(22)2/h3-12,31H,1-2H3,(H,26,27)(H,28,30)
InChIKeySCEVBRBKKQZTKM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cn1ccc2cc(ccc12)c3cc4nc([nH]c4cc3Cl)Oc5ccc(C)c(c5)C(=O)NO
ACDLabs 12.01c15c(ccc(c1)c2c(Cl)cc3c(c2)nc(n3)Oc4cc(c(cc4)C)C(=O)NO)n(C)cc5
OpenEye OEToolkits 2.0.6Cc1ccc(cc1C(=O)NO)Oc2[nH]c3cc(c(cc3n2)c4ccc5c(c4)ccn5C)Cl
FormulaC24 H19 Cl N4 O3
Name5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide
ChEMBL
DrugBank
ZINC
PDB chain6c9j Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6c9j Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states.
Resolution3.05 Å
Binding residue
(original residue number in PDB)		V13 L20 K33 K53 D90
Binding residue
(residue number reindexed from 1)		V3 L10 K23 K43 D80
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D141 K143 E145 N146 D159 S178
Catalytic site (residue number reindexed from 1) D131 K133 E135 N136 D149 S168
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
2.7.11.26: [tau protein] kinase.
2.7.11.31: [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004679 AMP-activated protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6c9j, PDBe:6c9j, PDBj:6c9j
PDBsum6c9j
PubMed30478170
UniProtQ13131|AAPK1_HUMAN 5'-AMP-activated protein kinase catalytic subunit alpha-1 (Gene Name=PRKAA1)

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