Structure of PDB 5m53 Chain A Binding Site BS01

Receptor Information
>5m53 Chain A (length=255) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DYEVLYTIGTGSYGRCQKIRRGKILVWKELDYGSMTEAEKQMLVSEVNLL
RELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLD
EEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGD
FGLVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKE
LAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILE
HHHHH
Ligand information
Ligand ID7GJ
InChIInChI=1S/C21H26N6O2/c1-27(2)20(28)15-9-6-10-16(11-15)24-21-25-18-17(22-13-23-18)19(26-21)29-12-14-7-4-3-5-8-14/h6,9-11,13-14H,3-5,7-8,12H2,1-2H3,(H2,22,23,24,25,26)
InChIKeyHZNQONMMEIJNNU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN(C)C(=O)c1cccc(Nc2nc(OCC3CCCCC3)c4[nH]cnc4n2)c1
OpenEye OEToolkits 2.0.6CN(C)C(=O)c1cccc(c1)Nc2nc3c(c(n2)OCC4CCCCC4)[nH]cn3
FormulaC21 H26 N6 O2
Name3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N},~{N}-dimethyl-benzamide
ChEMBL
DrugBank
ZINCZINC000584905386
PDB chain5m53 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5m53 Structure-guided design of purine-based probes for selective Nek2 inhibition.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		I14 Y19 K37 E87 Y88 C89 G92 D93 F148
Binding residue
(residue number reindexed from 1)		I8 Y13 K28 E78 Y79 C80 G83 D84 F139
Annotation score1
Binding affinityMOAD: ic50=0.62uM
PDBbind-CN: -logKd/Ki=6.21,IC50=0.62uM
Enzymatic activity
Catalytic site (original residue number in PDB) D141 K143 A145 N146 D159 T179
Catalytic site (residue number reindexed from 1) D132 K134 A136 N137 D150 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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5m53, PDBe:5m53, PDBj:5m53
PDBsum5m53
PubMed27833088
UniProtP51955|NEK2_HUMAN Serine/threonine-protein kinase Nek2 (Gene Name=NEK2)

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