Structure of PDB 5uvf Chain D Binding Site BS01

Receptor Information
>5uvf Chain D (length=296) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGEIITDMAAAAWKVGLPIGCIYLADMDAPCVVKVEPSGPLFTELKFYQR
AAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDRFMIMDRFGSDLQKIYEAN
AKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYL
VDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLE
ILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANA
PGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDL
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 D Residue 403 [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)		I43 V69 K71 M131 D132 R133 F134 L184 V196
Binding residue
(residue number reindexed from 1)		I19 V32 K34 M86 D87 R88 F89 L139 V151
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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