Structure of PDB 4dgm Chain A Binding Site BS01

Receptor Information
>4dgm Chain A (length=326) Species: 4577 (Zea mays) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKARVYADVNVLRPKEYWDYEALTVQWGEQDDYEVVRKVGRGKYSEVFEG
INVNNNEKCIIKILKPVKKKKIKREIKILQNLMGGPNIVKLLDIVRDQHS
KTPSLIFEYVNNTDFKVLYPTLTDYDIRYYIYELLKALDYCHSQGIMHRD
VKPHNVMIDHELRKLRLIDWGLAEFYHPGKEYNVRVASRYFKGPELLVDL
QDYDYSLDMWSLGCMFAGMIFRKEPFFYGHDNHDQLVKIAKVLGTDGLNV
YLNKYRIELDPQLEALVGRHSRKPWLKFMNADNQHLVSPEAIDFLDKLLR
YDHQERLTALEAMTHPYFQQVRAAEN
Ligand information
Ligand IDAGI
InChIInChI=1S/C15H10O5/c16-9-3-1-8(2-4-9)13-7-12(19)15-11(18)5-10(17)6-14(15)20-13/h1-7,16-18H
InChIKeyKZNIFHPLKGYRTM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Oc1ccc(cc1)C2=CC(=O)c3c(O)cc(O)cc3O2
OpenEye OEToolkits 1.5.0c1cc(ccc1C2=CC(=O)c3c(cc(cc3O2)O)O)O
ACDLabs 10.04O=C1c3c(OC(=C1)c2ccc(O)cc2)cc(O)cc3O
FormulaC15 H10 O5
Name5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one;
Apigenin
ChEMBLCHEMBL28
DrugBankDB07352
ZINCZINC000003871576
PDB chain4dgm Chain A Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dgm Inhibition of protein kinase CK2 by flavonoids and tyrphostins. A structural insight.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		V45 I66 K68 F113 V116 N118 M163 I174 D175
Binding residue
(residue number reindexed from 1)		V39 I60 K62 F107 V110 N112 M157 I168 D169
Annotation score1
Binding affinityMOAD: ic50=1.2uM
PDBbind-CN: -logKd/Ki=5.92,IC50=1.2uM
Enzymatic activity
Catalytic site (original residue number in PDB) D156 K158 N161 D175 S194
Catalytic site (residue number reindexed from 1) D150 K152 N155 D169 S188
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
GO:0044024 histone H2AS1 kinase activity
GO:0106310 protein serine kinase activity
Biological Process
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0016310 phosphorylation
GO:0051726 regulation of cell cycle
Cellular Component
GO:0005634 nucleus
GO:0005829 cytosol
GO:0005956 protein kinase CK2 complex
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:4dgm, PDBe:4dgm, PDBj:4dgm
PDBsum4dgm
PubMed22794353
UniProtP28523|CSK2A_MAIZE Casein kinase II subunit alpha (Gene Name=ACK2)

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