Structure of PDB 2xnn Chain A Binding Site BS01

Receptor Information
>2xnn 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]
SRAEDYEVLYTIGTYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVS
EVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKE
RQYLDEEFVLRVMTQLTLALKECHRRSRDLKPANVFLDGKQNVKLGDFGF
VGTPYYMSPEQMNRYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKI
REGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHH
H
Ligand information
Ligand ID430
InChIInChI=1S/C21H16F3N3O2S/c1-12(13-6-2-3-7-14(13)21(22,23)24)29-17-10-18(30-19(17)20(25)28)27-11-26-15-8-4-5-9-16(15)27/h2-12H,1H3,(H2,25,28)/t12-/m1/s1
InChIKeySQYKBXHMNBHADB-GFCCVEGCSA-N
SMILES
SoftwareSMILES
CACTVS 3.352C[CH](Oc1cc(sc1C(N)=O)n2cnc3ccccc23)c4ccccc4C(F)(F)F
ACDLabs 10.04FC(F)(F)c1ccccc1C(Oc4c(sc(n3cnc2ccccc23)c4)C(=O)N)C
OpenEye OEToolkits 1.6.1CC(c1ccccc1C(F)(F)F)Oc2cc(sc2C(=O)N)n3cnc4c3cccc4
OpenEye OEToolkits 1.6.1C[C@H](c1ccccc1C(F)(F)F)Oc2cc(sc2C(=O)N)n3cnc4c3cccc4
CACTVS 3.352C[C@@H](Oc1cc(sc1C(N)=O)n2cnc3ccccc23)c4ccccc4C(F)(F)F
FormulaC21 H16 F3 N3 O2 S
Name5-(1H-benzimidazol-1-yl)-3-{(1R)-1-[2-(trifluoromethyl)phenyl]ethoxy}thiophene-2-carboxamide
ChEMBL
DrugBank
ZINCZINC000064746576
PDB chain2xnn 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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PDB2xnn 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.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		I14 C22 K37 Y88 C89 D93 A145 F148 D159
Binding residue
(residue number reindexed from 1)		I12 C18 K33 Y84 C85 D89 A133 F136 D147
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.30,IC50>50uM
BindingDB: IC50=>50000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D141 K143 A145 N146 D159 T179
Catalytic site (residue number reindexed from 1) D129 K131 A133 N134 D147 T153
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:2xnn, PDBe:2xnn, PDBj:2xnn
PDBsum2xnn
PubMed21366329
UniProtP51955|NEK2_HUMAN Serine/threonine-protein kinase Nek2 (Gene Name=NEK2)

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