Structure of PDB 2xnm Chain A Binding Site BS01

Receptor Information
>2xnm Chain A (length=258) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQML
VSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGT
KERQYLDEEFVLRVMTQLTLALKECHRRRDLKPANVFLDGKQNVKLGDFG
LARILFVGTPYYMSPEQMNRSYNEKSDIWSLGCLLYELCALMPPFTAFSQ
KELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLI
LEHHHHHH
Ligand information
Ligand IDWGZ
InChIInChI=1S/C27H27F3N4O3S/c1-16(19-5-3-4-6-20(19)27(28,29)30)36-23-14-24(38-25(23)26(31)35)34-15-32-21-8-7-18(13-22(21)34)37-17-9-11-33(2)12-10-17/h3-8,13-17H,9-12H2,1-2H3,(H2,31,35)/t16-/m1/s1
InChIKeySWIVJTVGOIXUKC-MRXNPFEDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1CC(c1ccccc1C(F)(F)F)Oc2cc(sc2C(=O)N)n3cnc4c3cc(cc4)OC5CCN(CC5)C
CACTVS 3.352C[CH](Oc1cc(sc1C(N)=O)n2cnc3ccc(OC4CCN(C)CC4)cc23)c5ccccc5C(F)(F)F
ACDLabs 10.04FC(F)(F)c1ccccc1C(Oc5c(sc(n4cnc3ccc(OC2CCN(C)CC2)cc34)c5)C(=O)N)C
OpenEye OEToolkits 1.6.1C[C@H](c1ccccc1C(F)(F)F)Oc2cc(sc2C(=O)N)n3cnc4c3cc(cc4)OC5CCN(CC5)C
CACTVS 3.352C[C@@H](Oc1cc(sc1C(N)=O)n2cnc3ccc(OC4CCN(C)CC4)cc23)c5ccccc5C(F)(F)F
FormulaC27 H27 F3 N4 O3 S
Name5-{6-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-3-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}THIOPHENE-2-CARBOXAMIDE
ChEMBLCHEMBL1615278
DrugBank
ZINCZINC000059716256
PDB chain2xnm 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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PDB2xnm 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.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		I14 C22 K37 Y88 C89 D93 F148 G158 D159
Binding residue
(residue number reindexed from 1)		I12 C20 K35 Y86 C87 D91 F137 G147 D148
Annotation score1
Binding affinityMOAD: ic50=0.16uM
PDBbind-CN: -logKd/Ki=6.80,IC50=0.16uM
BindingDB: IC50=25nM
Enzymatic activity
Catalytic site (original residue number in PDB) D141 K143 A145 N146 D159 T179
Catalytic site (residue number reindexed from 1) D130 K132 A134 N135 D148 T159
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:2xnm, PDBe:2xnm, PDBj:2xnm
PDBsum2xnm
PubMed21366329
UniProtP51955|NEK2_HUMAN Serine/threonine-protein kinase Nek2 (Gene Name=NEK2)

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