Structure of PDB 2xk8 Chain A Binding Site BS01

Receptor Information
>2xk8 Chain A (length=246) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRAEDYEVLYTIGTRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEV
NLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQ
YLDEEFVLRVMTQLTLALKECHRRSRDLKPANVFLDGKQNVKLGDFFVGT
PYYMSPEQMNNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKF
RRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
Ligand information
Ligand ID5R1
InChIInChI=1S/C21H21N3O6/c1-27-15-7-11(5-6-13(15)21(25)26)18-20(22)23-10-14(24-18)12-8-16(28-2)19(30-4)17(9-12)29-3/h5-10H,1-4H3,(H2,22,23)(H,25,26)
InChIKeyQYMUPWSODGEMOO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1COc1cc(ccc1C(=O)O)c2c(ncc(n2)c3cc(c(c(c3)OC)OC)OC)N
CACTVS 3.352COc1cc(cc(OC)c1OC)c2cnc(N)c(n2)c3ccc(C(O)=O)c(OC)c3
ACDLabs 10.04O=C(O)c1ccc(cc1OC)c2nc(cnc2N)c3cc(OC)c(OC)c(OC)c3
FormulaC21 H21 N3 O6
Name4-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]-2-methoxybenzoic acid
ChEMBLCHEMBL1230435
DrugBank
ZINCZINC000058638560
PDB chain2xk8 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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PDB2xk8 Aminopyrazine Inhibitors Binding to an Unusual Inactive Conformation of the Mitotic Kinase Nek2: Sar and Structural Characterization.
Resolution2.001 Å
Binding residue
(original residue number in PDB)		I14 C22 K37 V68 Y70 M86 Y88 C89 G92 F148 D159 F160
Binding residue
(residue number reindexed from 1)		I12 C16 K31 V62 Y64 M80 Y82 C83 G86 F134 D145 F146
Annotation score1
Binding affinityMOAD: ic50=2.4uM
PDBbind-CN: -logKd/Ki=5.62,IC50=2.4uM
BindingDB: IC50=1300nM
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 T150
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:2xk8, PDBe:2xk8, PDBj:2xk8
PDBsum2xk8
PubMed20936789
UniProtP51955|NEK2_HUMAN Serine/threonine-protein kinase Nek2 (Gene Name=NEK2)

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