Structure of PDB 4qfs Chain A Binding Site BS02

Receptor Information
>4qfs Chain A (length=362) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVV
GKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKN
GRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADF
GLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALL
CGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRAT
IKDIREHEWFKQDLPKYLFKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWK
VVNPYYLRVRRKNPVTSTFSKMSLQLYQVDSRTYLLDFRSIDDSHTIEFF
EMCANLIKILAQ
Ligand information
Ligand ID32H
InChIInChI=1S/C14H6Br2N2O2S/c15-7-3-1-6(2-4-7)9-10-11(19)8(5-17)13(20)18-14(10)21-12(9)16/h1-4H,(H2,18,19,20)
InChIKeyBLJQBTCHXOTSEZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC1=C(C#N)C(=O)Nc2sc(Br)c(c3ccc(Br)cc3)c12
OpenEye OEToolkits 1.7.6c1cc(ccc1c2c3c(sc2Br)NC(=O)C(=C3O)C#N)Br
ACDLabs 12.01Brc3ccc(c1c2C(O)=C(C#N)C(=O)Nc2sc1Br)cc3
FormulaC14 H6 Br2 N2 O2 S
Name2-bromo-3-(4-bromophenyl)-4-hydroxy-6-oxo-6,7-dihydrothieno[2,3-b]pyridine-5-carbonitrile;
Br2-A769662core
ChEMBL
DrugBank
ZINCZINC000098208385
PDB chain4qfs Chain A Residue 602 [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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PDB4qfs Structural Basis for AMPK Activation: Natural and Synthetic Ligands Regulate Kinase Activity from Opposite Poles by Different Molecular Mechanisms.
Resolution3.55 Å
Binding residue
(original residue number in PDB)		K29 K31 I46 K51 D88 F90
Binding residue
(residue number reindexed from 1)		K21 K23 I38 K43 D80 F82
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.05,Kd=0.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) D139 K141 E143 N144 D157 S176
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:0003682 chromatin binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004679 AMP-activated protein kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0042557 eukaryotic elongation factor-2 kinase activator activity
GO:0044024 histone H2AS1 kinase activity
GO:0044877 protein-containing complex binding
GO:0046872 metal ion binding
GO:0047322 [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity
GO:0050321 tau-protein kinase activity
GO:0106310 protein serine kinase activity
GO:0140823 histone H2BS36 kinase activity
Biological Process
GO:0002842 positive regulation of T cell mediated immune response to tumor cell
GO:0006006 glucose metabolic 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:0008284 positive regulation of cell population proliferation
GO:0008610 lipid biosynthetic process
GO:0009410 response to xenobiotic stimulus
GO:0009411 response to UV
GO:0009631 cold acclimation
GO:0010332 response to gamma radiation
GO:0010508 positive regulation of autophagy
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0014823 response to activity
GO:0016055 Wnt signaling pathway
GO:0016310 phosphorylation
GO:0017148 negative regulation of translation
GO:0019395 fatty acid oxidation
GO:0031000 response to caffeine
GO:0031669 cellular response to nutrient levels
GO:0032007 negative regulation of TOR signaling
GO:0033554 cellular response to stress
GO:0034599 cellular response to oxidative stress
GO:0042149 cellular response to glucose starvation
GO:0042542 response to hydrogen peroxide
GO:0042593 glucose homeostasis
GO:0042752 regulation of circadian rhythm
GO:0043066 negative regulation of apoptotic process
GO:0043627 response to estrogen
GO:0045722 positive regulation of gluconeogenesis
GO:0045821 positive regulation of glycolytic process
GO:0045893 positive regulation of DNA-templated transcription
GO:0046321 positive regulation of fatty acid oxidation
GO:0046326 positive regulation of D-glucose import
GO:0046627 negative regulation of insulin receptor signaling pathway
GO:0048511 rhythmic process
GO:0048643 positive regulation of skeletal muscle tissue development
GO:0050870 positive regulation of T cell activation
GO:0050995 negative regulation of lipid catabolic process
GO:0055089 fatty acid homeostasis
GO:0060627 regulation of vesicle-mediated transport
GO:0061744 motor behavior
GO:0061762 CAMKK-AMPK signaling cascade
GO:0062028 regulation of stress granule assembly
GO:0070050 neuron cellular homeostasis
GO:0070301 cellular response to hydrogen peroxide
GO:0070507 regulation of microtubule cytoskeleton organization
GO:0071277 cellular response to calcium ion
GO:0071333 cellular response to glucose stimulus
GO:0071361 cellular response to ethanol
GO:0071380 cellular response to prostaglandin E stimulus
GO:0071456 cellular response to hypoxia
GO:0071466 cellular response to xenobiotic stimulus
GO:0097009 energy homeostasis
GO:1903109 positive regulation of mitochondrial transcription
GO:1903829 positive regulation of protein localization
GO:1903944 negative regulation of hepatocyte apoptotic process
GO:1903955 positive regulation of protein targeting to mitochondrion
GO:1904179 positive regulation of adipose tissue development
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:0000785 chromatin
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016324 apical plasma membrane
GO:0016607 nuclear speck
GO:0030424 axon
GO:0030425 dendrite
GO:0031588 nucleotide-activated protein kinase complex
GO:0032991 protein-containing complex
GO:0043025 neuronal cell body

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Biological Process
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Cellular Component
External links
PDB RCSB:4qfs, PDBe:4qfs, PDBj:4qfs
PDBsum4qfs
PubMed25066137
UniProtP54645|AAPK1_RAT 5'-AMP-activated protein kinase catalytic subunit alpha-1 (Gene Name=Prkaa1)

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