Structure of PDB 6npn Chain D Binding Site BS01

Receptor Information
>6npn Chain D (length=311) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFAVGEIITDMAAAAWKVGLPICIYLADMNSVGSDAPCVVKVEPSDNGPL
FTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMI
MDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKA
SNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSI
DAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRE
NIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKA
IGSKDDGKLDL
Ligand information
Ligand IDKWJ
InChIInChI=1S/C20H17N7O2/c1-4-8-26-12(3)19(29)27(9-5-2)16-11-21-20(23-17(16)26)22-13-6-7-14-15(10-13)24-25-18(14)28/h1-2,6-7,10-12H,8-9H2,3H3,(H,21,22,23)(H2,24,25,28)/t12-/m1/s1
InChIKeyGDTXGHSGLKEJJP-GFCCVEGCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C[C@@H]1C(=O)N(c2cnc(nc2N1CC#C)Nc3ccc4c(c3)NNC4=O)CC#C
OpenEye OEToolkits 2.0.6CC1C(=O)N(c2cnc(nc2N1CC#C)Nc3ccc4c(c3)NNC4=O)CC#C
ACDLabs 12.01C4(=O)C(C)N(CC#C)c3nc(Nc1cc2c(cc1)C(=O)NN2)ncc3N4CC#C
CACTVS 3.385C[C@H]1N(CC#C)c2nc(Nc3ccc4C(=O)NNc4c3)ncc2N(CC#C)C1=O
CACTVS 3.385C[CH]1N(CC#C)c2nc(Nc3ccc4C(=O)NNc4c3)ncc2N(CC#C)C1=O
FormulaC20 H17 N7 O2
Name(7R)-7-methyl-2-[(3-oxo-2,3-dihydro-1H-indazol-6-yl)amino]-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
ChEMBL
DrugBank
ZINC
PDB chain6npn Chain D 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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PDB6npn Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor
Resolution2.2 Å
Binding residue
(original residue number in PDB)		I43 I51 V69 E83 M131 D132 R133 F134 G135 L184 V196 D197
Binding residue
(residue number reindexed from 1)		I22 I24 V39 E53 M101 D102 R103 F104 G105 L154 V166 D167
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:6npn, PDBe:6npn, PDBj:6npn
PDBsum6npn
PubMed
UniProtQ99986|VRK1_HUMAN Serine/threonine-protein kinase VRK1 (Gene Name=VRK1)

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