Structure of PDB 5uvf Chain B Binding Site BS01

Receptor Information
>5uvf Chain B (length=316) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQFAVGEIITDMAAAAWKVGLPIGCIYLADMNSSESVGSDAPCVVKVEPS
DNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKS
YRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVH
GDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTI
EFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSK
IRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILL
QGLKAIGSKDDGKLDL
Ligand information
Ligand ID7DZ
InChIInChI=1S/C19H23F2N5O2/c1-10(2)5-6-26-11(3)18(28)25(4)15-9-22-19(24-17(15)26)23-12-7-13(20)16(27)14(21)8-12/h7-11,27H,5-6H2,1-4H3,(H,22,23,24)/t11-/m0/s1
InChIKeyDTEKTGDVSARYDS-NSHDSACASA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)CCN1[CH](C)C(=O)N(C)c2cnc(Nc3cc(F)c(O)c(F)c3)nc12
CACTVS 3.385CC(C)CCN1[C@@H](C)C(=O)N(C)c2cnc(Nc3cc(F)c(O)c(F)c3)nc12
ACDLabs 12.01CN3c1c(nc(nc1)Nc2cc(c(c(c2)F)O)F)N(CCC(C)C)C(C3=O)C
OpenEye OEToolkits 2.0.6C[C@H]1C(=O)N(c2cnc(nc2N1CCC(C)C)Nc3cc(c(c(c3)F)O)F)C
OpenEye OEToolkits 2.0.6CC1C(=O)N(c2cnc(nc2N1CCC(C)C)Nc3cc(c(c(c3)F)O)F)C
FormulaC19 H23 F2 N5 O2
Name(7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one;
BI-D1870
ChEMBL
DrugBank
ZINCZINC000033359422
PDB chain5uvf Chain B Residue 402 [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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PDB5uvf Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		M131 D132 F134
Binding residue
(residue number reindexed from 1)		M106 D107 F109
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:5uvf, PDBe:5uvf, PDBj:5uvf
PDBsum5uvf
PubMed28790404
UniProtQ99986|VRK1_HUMAN Serine/threonine-protein kinase VRK1 (Gene Name=VRK1)

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