Structure of PDB 6e4w Chain A Binding Site BS02

Receptor Information
>6e4w 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 IDHUG
InChIInChI=1S/C26H25F2NO9/c27-14-9-15-18(19(28)17(14)12-6-4-11(5-7-12)16-3-1-2-8-36-16)13(10-29-15)25(35)38-26-22(32)20(30)21(31)23(37-26)24(33)34/h4-7,9-10,16,20-23,26,29-32H,1-3,8H2,(H,33,34)/t16-,20-,21-,22+,23-,26-/m0/s1
InChIKeyGZCJKJJWOUAGMR-WBTGXFMPSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c4c(ccc(c3c(cc1c(c(cn1)C(=O)OC2C(C(O)C(C(O2)C(=O)O)O)O)c3F)F)c4)C5OCCCC5
OpenEye OEToolkits 2.0.6c1cc(ccc1c2c(cc3c(c2F)c(c[nH]3)C(=O)O[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)C(=O)O)O)O)O)F)[C@@H]5CCCCO5
CACTVS 3.385O[CH]1[CH](O)[CH](O[CH]([CH]1O)C(O)=O)OC(=O)c2c[nH]c3cc(F)c(c(F)c23)c4ccc(cc4)[CH]5CCCCO5
OpenEye OEToolkits 2.0.6c1cc(ccc1c2c(cc3c(c2F)c(c[nH]3)C(=O)OC4C(C(C(C(O4)C(=O)O)O)O)O)F)C5CCCCO5
CACTVS 3.385O[C@@H]1[C@@H](O)[C@@H](O[C@@H]([C@H]1O)C(O)=O)OC(=O)c2c[nH]c3cc(F)c(c(F)c23)c4ccc(cc4)[C@@H]5CCCCO5
FormulaC26 H25 F2 N O9
Name1-O-(4,6-difluoro-5-{4-[(2S)-oxan-2-yl]phenyl}-1H-indole-3-carbonyl)-beta-D-glucopyranuronic acid
ChEMBLCHEMBL4246000
DrugBank
ZINC
PDB chain6e4w Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6e4w Acyl Glucuronide Metabolites of 6-Chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1 H-indole-3-carboxylic Acid (PF-06409577) and Related Indole-3-carboxylic Acid Derivatives are Direct Activators of Adenosine Monophosphate-Activated Protein Kinase (AMPK).
Resolution3.35 Å
Binding residue
(original residue number in PDB)		L18 G19 K31 I46 D88
Binding residue
(residue number reindexed from 1)		L10 G11 K23 I38 D80
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.70,Kd=197.8nM
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:0004672 protein kinase activity
GO:0004679 AMP-activated protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

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Molecular Function
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Biological Process
External links
PDB RCSB:6e4w, PDBe:6e4w, PDBj:6e4w
PDBsum6e4w
PubMed30036059
UniProtP54645|AAPK1_RAT 5'-AMP-activated protein kinase catalytic subunit alpha-1 (Gene Name=Prkaa1)

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