Structure of PDB 2xkd Chain A Binding Site BS01

Receptor Information
>2xkd Chain A (length=251) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRAEDYEVLYTIGTGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSE
VNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKER
QYLDEEFVLRVMTQLTLALKECHRRSDLKPANVFLDGKQNVKLGDFTFVG
TPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKI
REGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH
H
Ligand information
Ligand IDT3M
InChIInChI=1S/C20H19N3O5/c1-26-15-8-13(9-16(27-2)18(15)28-3)14-10-22-19(21)17(23-14)11-4-6-12(7-5-11)20(24)25/h4-10H,1-3H3,(H2,21,22)(H,24,25)
InChIKeyJOVBKEMPKRSFDQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352COc1cc(cc(OC)c1OC)c2cnc(N)c(n2)c3ccc(cc3)C(O)=O
OpenEye OEToolkits 1.6.1COc1cc(cc(c1OC)OC)c2cnc(c(n2)c3ccc(cc3)C(=O)O)N
ACDLabs 10.04O=C(O)c1ccc(cc1)c2nc(cnc2N)c3cc(OC)c(OC)c(OC)c3
FormulaC20 H19 N3 O5
Name4-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]benzoic acid
ChEMBLCHEMBL1236145
DrugBank
ZINCZINC000058650700
PDB chain2xkd Chain A Residue 1280 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2xkd Aminopyrazine Inhibitors Binding to an Unusual Inactive Conformation of the Mitotic Kinase Nek2: Sar and Structural Characterization.
Resolution1.96 Å
Binding residue
(original residue number in PDB)		I14 C22 K37 Y70 M86 Y88 C89 G92 F148 D159
Binding residue
(residue number reindexed from 1)		I12 C17 K32 Y65 M81 Y83 C84 G87 F134 D145
Annotation score1
Binding affinityMOAD: ic50=2.3uM
PDBbind-CN: -logKd/Ki=5.64,IC50=2.3uM
BindingDB: IC50=1600nM
Enzymatic activity
Catalytic site (original residue number in PDB) D141 K143 A145 N146 D159 T179
Catalytic site (residue number reindexed from 1) D127 K129 A131 N132 D145 T151
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2xkd, PDBe:2xkd, PDBj:2xkd
PDBsum2xkd
PubMed20936789
UniProtP51955|NEK2_HUMAN Serine/threonine-protein kinase Nek2 (Gene Name=NEK2)

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