Structure of PDB 6eip Chain A Binding Site BS01

Receptor Information
>6eip Chain A (length=342) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQE
WVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNH
LCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSI
IHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVL
LGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAH
ILDQAPKARKFFEKLPDGTWNLKKTEYKPPGTRKLHNILGVETGGPGGRR
AGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFK
Ligand information
Ligand IDB7B
InChIInChI=1S/C23H28N6O2/c1-28-19-13-25-23(26-15-11-9-14(10-12-15)20(24)30)27-21(19)29(16-5-2-3-6-16)18-8-4-7-17(18)22(28)31/h9-13,16-18H,2-8H2,1H3,(H2,24,30)(H,25,26,27)/t17-,18+/m0/s1
InChIKeyVJDBYVPTQWPRPA-ZWKOTPCHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CN1c2cnc(nc2N([C@@H]3CCC[C@@H]3C1=O)C4CCCC4)Nc5ccc(cc5)C(=O)N
CACTVS 3.385CN1C(=O)[CH]2CCC[CH]2N(C3CCCC3)c4nc(Nc5ccc(cc5)C(N)=O)ncc14
CACTVS 3.385CN1C(=O)[C@H]2CCC[C@H]2N(C3CCCC3)c4nc(Nc5ccc(cc5)C(N)=O)ncc14
OpenEye OEToolkits 2.0.6CN1c2cnc(nc2N(C3CCCC3C1=O)C4CCCC4)Nc5ccc(cc5)C(=O)N
FormulaC23 H28 N6 O2
Name4-[[(3~{R},7~{S})-2-cyclopentyl-9-methyl-8-oxidanylidene-2,9,12,14-tetrazatricyclo[8.4.0.0^{3,7}]tetradeca-1(14),10,12-trien-13-yl]amino]benzamide
ChEMBLCHEMBL3986079
DrugBank
ZINC
PDB chain6eip Chain A Residue 501 [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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PDB6eip Novel Scaffolds for Dual Specificity Tyrosine-Phosphorylation-Regulated Kinase (DYRK1A) Inhibitors.
Resolution2.56 Å
Binding residue
(original residue number in PDB)		I165 G166 V173 A186 V222 F238 M240 L241 N244 L294 V306
Binding residue
(residue number reindexed from 1)		I32 G33 V40 A53 V89 F105 M107 L108 N111 L161 V173
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.70,Ki=2015nM
BindingDB: Ki=2015nM,IC50=4200nM
Enzymatic activity
Catalytic site (original residue number in PDB) D287 K289 N292 D307 S324
Catalytic site (residue number reindexed from 1) D154 K156 N159 D174 S191
Enzyme Commision number 2.7.11.23: [RNA-polymerase]-subunit kinase.
2.7.12.1: dual-specificity kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004712 protein serine/threonine/tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0046777 protein autophosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6eip, PDBe:6eip, PDBj:6eip
PDBsum6eip
PubMed30095246
UniProtQ13627|DYR1A_HUMAN Dual specificity tyrosine-phosphorylation-regulated kinase 1A (Gene Name=DYRK1A)

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