Structure of PDB 2xnp Chain A Binding Site BS01

Receptor Information
>2xnp Chain A (length=253) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRAEDYEVLYTIGTGYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLV
SEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTK
ERQYLDEEFVLRVMTQLTLALKECHRRSHRDLKPANVFLDGKQNVKLGDF
GLFVGTPYYMSPEQMNRNEKSDIWSLGCLLYELCALMPPFTAFSQKELAG
KIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH
HHH
Ligand information
Ligand IDWCX
InChIInChI=1S/C29H29F3N4O3/c1-18(22-5-3-4-6-24(22)29(30,31)32)38-27-15-19(7-9-23(27)28(33)37)36-17-34-25-16-21(8-10-26(25)36)39-20-11-13-35(2)14-12-20/h3-10,15-18,20H,11-14H2,1-2H3,(H2,33,37)/t18-/m1/s1
InChIKeyFASALJZFFLCNKM-GOSISDBHSA-N
SMILES
SoftwareSMILES
CACTVS 3.352C[C@@H](Oc1cc(ccc1C(N)=O)n2cnc3cc(OC4CCN(C)CC4)ccc23)c5ccccc5C(F)(F)F
ACDLabs 10.04FC(F)(F)c1ccccc1C(Oc2c(C(=O)N)ccc(c2)n4c5ccc(OC3CCN(C)CC3)cc5nc4)C
OpenEye OEToolkits 1.6.1CC(c1ccccc1C(F)(F)F)Oc2cc(ccc2C(=O)N)n3cnc4c3ccc(c4)OC5CCN(CC5)C
OpenEye OEToolkits 1.6.1C[C@H](c1ccccc1C(F)(F)F)Oc2cc(ccc2C(=O)N)n3cnc4c3ccc(c4)OC5CCN(CC5)C
CACTVS 3.352C[CH](Oc1cc(ccc1C(N)=O)n2cnc3cc(OC4CCN(C)CC4)ccc23)c5ccccc5C(F)(F)F
FormulaC29 H29 F3 N4 O3
Name4-{5-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-2-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}BENZAMIDE
ChEMBLCHEMBL1615277
DrugBank
ZINCZINC000064744235
PDB chain2xnp 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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PDB2xnp 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 G15 Y19 C22 Y88 C89 E90 G92 D93 F148 G158 D159 F160
Binding residue
(residue number reindexed from 1)		I12 G13 Y16 C19 Y85 C86 E87 G89 D90 F138 G148 D149 F150
Annotation score1
Binding affinityMOAD: ic50=0.36uM
PDBbind-CN: -logKd/Ki=6.44,IC50=0.36uM
BindingDB: IC50=570nM
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 T156
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:2xnp, PDBe:2xnp, PDBj:2xnp
PDBsum2xnp
PubMed21366329
UniProtP51955|NEK2_HUMAN Serine/threonine-protein kinase Nek2 (Gene Name=NEK2)

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