Structure of PDB 2xno Chain A Binding Site BS01

Receptor Information
>2xno 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]
SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQML
VSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGT
KERQYLDEEFVLRVMTQLTLALKECHRRSRDLKPANVFLDGKQNVKLGDF
FVGTPYYMSPEQMNRNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKI
REGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH
H
Ligand information
Ligand IDED8
InChIInChI=1S/C26H25F3N4O3S/c1-32-10-8-17(9-11-32)36-18-6-7-20-21(12-18)33(15-31-20)23-13-22(24(37-23)25(30)34)35-14-16-4-2-3-5-19(16)26(27,28)29/h2-7,12-13,15,17H,8-11,14H2,1H3,(H2,30,34)
InChIKeyFNHUNERGHGEZMB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CN1CCC(CC1)Oc2ccc3c(c2)n(cn3)c4cc(c(s4)C(=O)N)OCc5ccccc5C(F)(F)F
ACDLabs 12.01FC(F)(F)c1ccccc1COc5c(sc(n4cnc3ccc(OC2CCN(C)CC2)cc34)c5)C(=O)N
CACTVS 3.370CN1CCC(CC1)Oc2ccc3ncn(c4sc(C(N)=O)c(OCc5ccccc5C(F)(F)F)c4)c3c2
FormulaC26 H25 F3 N4 O3 S
Name5-{6-[(1-methylpiperidin-4-yl)oxy]-1H-benzimidazol-1-yl}-3-{[2-(trifluoromethyl)benzyl]oxy}thiophene-2-carboxamide
ChEMBLCHEMBL1614933
DrugBank
ZINCZINC000064746655
PDB chain2xno 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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PDB2xno Benzimidazole Inhibitors Induce a Dfg-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure-Activity Relationship.
Resolution1.98 Å
Binding residue
(original residue number in PDB)		I14 C22 K37 M86 Y88 C89 D93 A145 F148 D159
Binding residue
(residue number reindexed from 1)		I12 C20 K35 M84 Y86 C87 D91 A135 F138 D149
Annotation score1
Binding affinityMOAD: ic50=1.18uM
PDBbind-CN: -logKd/Ki=5.93,IC50=1.18uM
BindingDB: IC50=1180nM
Enzymatic activity
Catalytic site (original residue number in PDB) D141 K143 A145 N146 D159 T179
Catalytic site (residue number reindexed from 1) D131 K133 A135 N136 D149 T154
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

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Molecular Function
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Biological Process
External links
PDB RCSB:2xno, PDBe:2xno, PDBj:2xno
PDBsum2xno
PubMed21366329
UniProtP51955|NEK2_HUMAN Serine/threonine-protein kinase Nek2 (Gene Name=NEK2)

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