Structure of PDB 4cfe Chain C Binding Site BS02

Receptor Information
>4cfe Chain C (length=404) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVKIGHYVLGDTLGVGTFGKVKIGEHQLTGHKVAVKILNRQKIRSLDVVG
KIKREIQNLKLFRHPHIIKLYQVISTPTDFFMVMEYVSGGELFDYICKHG
RVEEMEARRLFQQILSAVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFG
LSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSCGVILYALLC
GTLPFDDEHVPTLFKKIRGGVFYIPEYLNRSVATLLMHMLQVDPLKRATI
KDIREHEWFKQDLPSYLFPEDPSYDIIDNRRIMNQASEFYLASSPLKPHP
ERMPPLAVKKAKWHLGIRSQSKPYDIMAEVYRAMKQLDFEWKVVNAYHLR
VRRKNPVTGNYVKMSLQLYLVDNRSYLLDFKSIDLGSHTMDFFEMCASLI
TTLA
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
Global viewLocal viewStructure summary

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PDB4cfe Structural Basis of Ampk Regulation by Small Molecule Activators.
Resolution3.023 Å
Binding residue
(original residue number in PDB)		K29 K31 I46 N48 D88
Binding residue
(residue number reindexed from 1)		K20 K22 I37 N39 D79
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.22,Kd=0.06uM
Enzymatic activity
Catalytic site (original residue number in PDB) D139 K141 E143 N144 D157 S176
Catalytic site (residue number reindexed from 1) D130 K132 E134 N135 D148 S167
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
2.7.11.31: [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase.
Gene Ontology
Molecular Function
GO:0003682 chromatin binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004679 AMP-activated protein kinase activity
GO:0004712 protein serine/threonine/tyrosine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0044024 histone H2AS1 kinase activity
GO:0046872 metal ion binding
GO:0047322 [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity
GO:0106310 protein serine kinase activity
GO:0140823 histone H2BS36 kinase activity
Biological Process
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0006633 fatty acid biosynthetic process
GO:0006695 cholesterol biosynthetic process
GO:0006914 autophagy
GO:0007165 signal transduction
GO:0008610 lipid biosynthetic process
GO:0010468 regulation of gene expression
GO:0010508 positive regulation of autophagy
GO:0010629 negative regulation of gene expression
GO:0014850 response to muscle activity
GO:0016055 Wnt signaling pathway
GO:0016239 positive regulation of macroautophagy
GO:0016241 regulation of macroautophagy
GO:0016310 phosphorylation
GO:0031669 cellular response to nutrient levels
GO:0032007 negative regulation of TOR signaling
GO:0034599 cellular response to oxidative stress
GO:0042149 cellular response to glucose starvation
GO:0042593 glucose homeostasis
GO:0042752 regulation of circadian rhythm
GO:0043066 negative regulation of apoptotic process
GO:0045821 positive regulation of glycolytic process
GO:0048511 rhythmic process
GO:0055089 fatty acid homeostasis
GO:0062028 regulation of stress granule assembly
GO:0070507 regulation of microtubule cytoskeleton organization
GO:0071277 cellular response to calcium ion
GO:0071333 cellular response to glucose stimulus
GO:0071380 cellular response to prostaglandin E stimulus
GO:0071466 cellular response to xenobiotic stimulus
GO:0097009 energy homeostasis
GO:1903829 positive regulation of protein localization
GO:1903944 negative regulation of hepatocyte apoptotic process
GO:1904262 negative regulation of TORC1 signaling
GO:1904428 negative regulation of tubulin deacetylation
GO:1905691 lipid droplet disassembly
GO:1990044 protein localization to lipid droplet
GO:2000758 positive regulation of peptidyl-lysine acetylation
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0010494 cytoplasmic stress granule
GO:0016607 nuclear speck
GO:0030424 axon
GO:0030425 dendrite
GO:0031588 nucleotide-activated protein kinase complex
GO:0043025 neuronal cell body

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4cfe, PDBe:4cfe, PDBj:4cfe
PDBsum4cfe
PubMed24352254
UniProtP54646|AAPK2_HUMAN 5'-AMP-activated protein kinase catalytic subunit alpha-2 (Gene Name=PRKAA2)

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