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Structure of PDB 2xkf Chain A Binding Site BS01

Receptor Information
>2xkf Chain A (length=250) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRAEDYEVLYTIGTGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSE
VNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKER
QYLDEEFVLRVMTQLTLALKECHRRSRDLKPANVFLDGKQNVKLGDFFVG
TPYYMSPEQMNRSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIR
EGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
Ligand information
Ligand IDBX1
InChIInChI=1S/C19H24N4O5/c1-26-14-8-12(9-15(27-2)16(14)28-3)13-10-21-17(20)18(22-13)23-6-4-11(5-7-23)19(24)25/h8-11H,4-7H2,1-3H3,(H2,20,21)(H,24,25)
InChIKeyFFHSQDAETWTILU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1COc1cc(cc(c1OC)OC)c2cnc(c(n2)N3CCC(CC3)C(=O)O)N
CACTVS 3.352COc1cc(cc(OC)c1OC)c2cnc(N)c(n2)N3CCC(CC3)C(O)=O
ACDLabs 10.04O=C(O)C3CCN(c2nc(c1cc(OC)c(OC)c(OC)c1)cnc2N)CC3
FormulaC19 H24 N4 O5
Name1-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]piperidine-4-carboxylic acid
ChEMBLCHEMBL1231522
DrugBank
ZINCZINC000058660889
PDB chain2xkf Chain A Residue 1280 [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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PDB2xkf Aminopyrazine Inhibitors Binding to an Unusual Inactive Conformation of the Mitotic Kinase Nek2: Sar and Structural Characterization.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		I14 K37 Y70 M86 Y88 C89 G92 D93 F148 D159
Binding residue
(residue number reindexed from 1)		I12 K32 Y65 M81 Y83 C84 G87 D88 F135 D146
Annotation score1
Binding affinityMOAD: ic50=0.87uM
PDBbind-CN: -logKd/Ki=6.06,IC50=0.87uM
BindingDB: IC50=410nM
Enzymatic activity
Catalytic site (original residue number in PDB) D141 K143 A145 N146 D159 T179
Catalytic site (residue number reindexed from 1) D128 K130 A132 N133 D146 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
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Biological Process
External links
PDB RCSB:2xkf, PDBe:2xkf, PDBj:2xkf
PDBsum2xkf
PubMed20936789
UniProtP51955|NEK2_HUMAN Serine/threonine-protein kinase Nek2 (Gene Name=NEK2)

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