Structure of PDB 3op5 Chain B Binding Site BS01

Receptor Information
>3op5 Chain B (length=319) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQFAVGEIITDMAAAAWKVGLPIGQFGCIYLADMNSSESVGSDAPCVVKV
EPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKN
GKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHE
YVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHD
GTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVR
DSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRD
ILLQGLKAIGSKDDGKLDL
Ligand information
Ligand IDREB
InChIInChI=1S/C18H17N7/c19-9-7-12-1-5-14(6-2-12)21-18-20-10-8-16(23-18)22-17-11-15(24-25-17)13-3-4-13/h1-2,5-6,8,10-11,13H,3-4,7H2,(H3,20,21,22,23,24,25)
InChIKeyYRRRHSNOXWKVDL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01N#CCc1ccc(cc1)Nc4nc(Nc2nnc(c2)C3CC3)ccn4
OpenEye OEToolkits 1.7.0c1cc(ccc1CC#N)Nc2nccc(n2)Nc3cc([nH]n3)C4CC4
CACTVS 3.370N#CCc1ccc(Nc2nccc(Nc3cc([nH]n3)C4CC4)n2)cc1
FormulaC18 H17 N7
Name[4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile
ChEMBLCHEMBL1235645
DrugBank
ZINCZINC000058651050
PDB chain3op5 Chain B Residue 365 [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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PDB3op5 Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Q45 F48 I51 V69 M131 D132 R133 F134
Binding residue
(residue number reindexed from 1)		Q25 F26 I29 V47 M109 D110 R111 F112
Annotation score1
Enzymatic activity
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:0016301 kinase activity
GO:0019901 protein kinase binding
GO:0031492 nucleosomal DNA binding
GO:0035175 histone H3S10 kinase activity
GO:0042393 histone binding
GO:0044024 histone H2AS1 kinase activity
GO:0072354 histone H3T3 kinase activity
GO:0106310 protein serine kinase activity
GO:0141003 histone H2AX kinase activity
Biological Process
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0006974 DNA damage response
GO:0007077 mitotic nuclear membrane disassembly
GO:0007165 signal transduction
GO:0016310 phosphorylation
GO:0030576 Cajal body organization
GO:0031175 neuron projection development
GO:0046777 protein autophosphorylation
GO:0051301 cell division
GO:0090166 Golgi disassembly
GO:0120187 positive regulation of protein localization to chromatin
GO:2001222 regulation of neuron migration
Cellular Component
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005795 Golgi stack
GO:0005829 cytosol
GO:0015030 Cajal body

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3op5, PDBe:3op5, PDBj:3op5
PDBsum3op5
PubMed28790404
UniProtQ99986|VRK1_HUMAN Serine/threonine-protein kinase VRK1 (Gene Name=VRK1)

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