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Structure of PDB 5cu3 Chain A Binding Site BS01

Receptor Information
>5cu3 Chain A (length=325) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSE
VFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVK
DPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGI
MHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPEL
LVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTE
DLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLD
KLLRYDHQSRLTAREAMEHPYFYTV
Ligand information
Ligand ID54S
InChIInChI=1S/C26H26ClN3O4/c27-23-15-18(9-10-22(23)19-5-2-1-3-6-19)17-28-13-11-24(31)29-14-12-25(32)30-21-8-4-7-20(16-21)26(33)34/h1-10,15-16,28H,11-14,17H2,(H,29,31)(H,30,32)(H,33,34)
InChIKeyNZDQDPKZQDWCOF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(CC(NCCC(Nc1cc(ccc1)C(O)=O)=O)=O)NCc2ccc(c(c2)Cl)c3ccccc3
OpenEye OEToolkits 1.9.2c1ccc(cc1)c2ccc(cc2Cl)CNCCC(=O)NCCC(=O)Nc3cccc(c3)C(=O)O
CACTVS 3.385OC(=O)c1cccc(NC(=O)CCNC(=O)CCNCc2ccc(c(Cl)c2)c3ccccc3)c1
FormulaC26 H26 Cl N3 O4
NameN-[(2-chlorobiphenyl-4-yl)methyl]-beta-alanyl-N-(3-carboxyphenyl)-beta-alaninamide
ChEMBLCHEMBL4070389
DrugBank
ZINCZINC000584905143
PDB chain5cu3 Chain A Residue 404 [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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PDB5cu3 Specific inhibition of CK2 alpha from an anchor outside the active site.
Resolution1.787 Å
Binding residue
(original residue number in PDB)		K68 F113 N118 F121 L124 L128 Y136 P159 H160 V162 I164 I174 D175 M225
Binding residue
(residue number reindexed from 1)		K66 F111 N116 F119 L122 L126 Y134 P157 H158 V160 I162 I172 D173 M223
Annotation score1
Binding affinityMOAD: Kd=0.32uM
BindingDB: Kd=320nM,IC50=670nM
Enzymatic activity
Catalytic site (original residue number in PDB) D156 K158 N161 D175 P184 S194
Catalytic site (residue number reindexed from 1) D154 K156 N159 D173 P182 S192
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
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5cu3, PDBe:5cu3, PDBj:5cu3
PDBsum5cu3
PubMed28451126
UniProtP68400|CSK21_HUMAN Casein kinase II subunit alpha (Gene Name=CSNK2A1)

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