Structure of PDB 5y86 Chain A Binding Site BS01

Receptor Information
>5y86 Chain A (length=395) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVPLTPEQALKQYKHHLTAYEKLEIINYPEIYFVGPNAKKRHGVIGGPNN
GGYDDADGAYIHVPRDHLAYRYEVLKIIGKGSFGQVARVYDHKLRQYVAL
KMVRNEKRFHRQAAEEIRILEHLKKQDKTGSMNVIHMLESFTFRNHVCMA
FELLSIDLYELIKKNKFQGFSVQLVRKFAQSILQSLDALHKNKIIHCDLK
PENILLKHHGRSSTKVIDFGSSCFEYQKLYTYIQSRFYRAPEIILGSRYS
TPIDIWSFGCILAELLTGQPLFPGEDEGDQLACMMELLGMPPPKLLEQSK
RAKYFINSKGIPRYCSVTTQADGRVVLVGGRSRRGKKRGPPGSKDWGTAL
KGCDDYLFIEFLKRCLHWDPSARLTPAQALRHPWISKSVPRPLTT
Ligand information
Ligand IDHRM
InChIInChI=1S/C13H12N2O/c1-8-13-11(5-6-14-8)10-4-3-9(16-2)7-12(10)15-13/h3-7,15H,1-2H3
InChIKeyBXNJHAXVSOCGBA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c2c(ccn1)c3ccc(cc3[nH]2)OC
CACTVS 3.341COc1ccc2c([nH]c3c(C)nccc23)c1
ACDLabs 10.04n3ccc2c1c(cc(OC)cc1)nc2c3C
FormulaC13 H12 N2 O
Name7-METHOXY-1-METHYL-9H-BETA-CARBOLINE;
7-METHOXY-1-METHYL-9H-PYRIDO[3,4-B]INDOL;
HARMINE
ChEMBLCHEMBL269538
DrugBankDB07919
ZINCZINC000018847046
PDB chain5y86 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5y86 Crystal Structure of Human Dual-Specificity Tyrosine-Regulated Kinase 3 Reveals New Structural Features and Insights into its Auto-phosphorylation
Resolution1.9 Å
Binding residue
(original residue number in PDB)		A236 K238 F288 L291 L342 I354
Binding residue
(residue number reindexed from 1)		A99 K101 F151 L154 L205 I217
Annotation score1
Binding affinityMOAD: ic50=0.8uM
PDBbind-CN: -logKd/Ki=6.10,IC50=0.8uM
BindingDB: IC50=800nM
Enzymatic activity
Catalytic site (original residue number in PDB) D335 K337 N340 D355 S372
Catalytic site (residue number reindexed from 1) D198 K200 N203 D218 S235
Enzyme Commision number 2.7.12.1: dual-specificity kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004712 protein serine/threonine/tyrosine kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0006468 protein phosphorylation
GO:0016310 phosphorylation
GO:0030218 erythrocyte differentiation
GO:0035063 nuclear speck organization
GO:0035617 stress granule disassembly
GO:0043066 negative regulation of apoptotic process
GO:0043518 negative regulation of DNA damage response, signal transduction by p53 class mediator
GO:0051301 cell division
GO:0080135 regulation of cellular response to stress
GO:1902751 positive regulation of cell cycle G2/M phase transition
GO:1903008 organelle disassembly
GO:1903432 regulation of TORC1 signaling
Cellular Component
GO:0000242 pericentriolar material
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0010494 cytoplasmic stress granule
GO:0016607 nuclear speck
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5y86, PDBe:5y86, PDBj:5y86
PDBsum5y86
PubMed29634919
UniProtO43781|DYRK3_HUMAN Dual specificity tyrosine-phosphorylation-regulated kinase 3 (Gene Name=DYRK3)

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