Structure of PDB 6cmm Chain D Binding Site BS01

Receptor Information
>6cmm Chain D (length=315) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FAVGEIITDMAAAAWKVGLPIGQCIYLADMNSSESVGSDAPCVVKVEPSD
NGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSY
RFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHG
DIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIE
FTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKI
RYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQ
GLKAIGSKDDGKLDL
Ligand information
Ligand IDF7D
InChIInChI=1S/C19H15F2N5O2/c1-4-6-25-11(3)18(28)26(7-5-2)15-10-22-19(24-17(15)25)23-12-8-13(20)16(27)14(21)9-12/h1-2,8-11,27H,6-7H2,3H3,(H,22,23,24)/t11-/m1/s1
InChIKeyKDZIESJUFYBJGD-LLVKDONJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1C(=O)N(c2cnc(nc2N1CC#C)Nc3cc(c(c(c3)F)O)F)CC#C
ACDLabs 12.01c12N(CC#C)C(=O)C(C)N(CC#C)c1nc(nc2)Nc3cc(F)c(O)c(c3)F
CACTVS 3.385C[CH]1N(CC#C)c2nc(Nc3cc(F)c(O)c(F)c3)ncc2N(CC#C)C1=O
CACTVS 3.385C[C@H]1N(CC#C)c2nc(Nc3cc(F)c(O)c(F)c3)ncc2N(CC#C)C1=O
OpenEye OEToolkits 2.0.6C[C@@H]1C(=O)N(c2cnc(nc2N1CC#C)Nc3cc(c(c(c3)F)O)F)CC#C
FormulaC19 H15 F2 N5 O2
Name(7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one
ChEMBL
DrugBank
ZINC
PDB chain6cmm 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6cmm Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine inhibitor
Resolution2.1 Å
Binding residue
(original residue number in PDB)		I43 V69 K71 M131 D132 R133 F134 D137 L184 V196
Binding residue
(residue number reindexed from 1)		I21 V43 K45 M105 D106 R107 F108 D111 L158 V170
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6cmm, PDBe:6cmm, PDBj:6cmm
PDBsum6cmm
PubMed
UniProtQ99986|VRK1_HUMAN Serine/threonine-protein kinase VRK1 (Gene Name=VRK1)

[Back to BioLiP]