Structure of PDB 5m56 Chain A Binding Site BS01

Receptor Information
>5m56 Chain A (length=331) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDGYQLVRKLGRGKY
SEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDT
VKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSK
GIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGP
ELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLG
TEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDL
LDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQ
Ligand information
Ligand ID7FC
InChIInChI=1S/C16H8Cl2O5/c17-9-5-10-12(19)13(20)14(23-15(10)11(18)6-9)7-1-3-8(4-2-7)16(21)22/h1-6,20H,(H,21,22)
InChIKeyCFWCAEJMOUILDR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(ccc1C2=C(C(=O)c3cc(cc(c3O2)Cl)Cl)O)C(=O)O
CACTVS 3.385OC(=O)c1ccc(cc1)C2=C(O)C(=O)c3cc(Cl)cc(Cl)c3O2
FormulaC16 H8 Cl2 O5
Name4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid
ChEMBL
DrugBank
ZINCZINC000031773452
PDB chain5m56 Chain A Residue 401 [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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PDB5m56 Structural Hypervariability of the Two Human Protein Kinase CK2 Catalytic Subunit Paralogs Revealed by Complex Structures with a Flavonol- and a Thieno[2,3-d]pyrimidine-Based Inhibitor.
Resolution2.237 Å
Binding residue
(original residue number in PDB)		L46 V67 K69 F114 E115 Y116 I117 M164 I175 D176
Binding residue
(residue number reindexed from 1)		L45 V66 K68 F113 E114 Y115 I116 M163 I174 D175
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.89,Ki=13nM
Enzymatic activity
Catalytic site (original residue number in PDB) I153 H155 V158 L172 V191
Catalytic site (residue number reindexed from 1) I152 H154 V157 L171 V190
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:0005515 protein binding
GO:0005524 ATP binding
GO:0044024 histone H2AS1 kinase activity
GO:0106310 protein serine kinase activity
Biological Process
GO:0006302 double-strand break repair
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0006915 apoptotic process
GO:0007283 spermatogenesis
GO:0016055 Wnt signaling pathway
GO:0016310 phosphorylation
GO:0021987 cerebral cortex development
GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0051726 regulation of cell cycle
GO:0097421 liver regeneration
GO:1901524 regulation of mitophagy
GO:1903955 positive regulation of protein targeting to mitochondrion
GO:1905818 regulation of chromosome separation
GO:2001234 negative regulation of apoptotic signaling pathway
Cellular Component
GO:0000785 chromatin
GO:0001669 acrosomal vesicle
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005956 protein kinase CK2 complex
GO:0031519 PcG protein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5m56, PDBe:5m56, PDBj:5m56
PDBsum5m56
PubMed28085026
UniProtP19784|CSK22_HUMAN Casein kinase II subunit alpha' (Gene Name=CSNK2A2)

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