Structure of PDB 5m55 Chain A Binding Site BS01

Receptor Information
>5m55 Chain A (length=240) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRAEDYEVLYTIGTRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEV
NLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQ
YLDEEFVLRVMTQLTLALKECHRRSLKPANVFLDGKQNVKLGDTPYYMSP
EQMNNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYR
YSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
Ligand information
Ligand ID7GG
InChIInChI=1S/C17H20N6/c1-3-23(4-2)11-10-14-15-16(19-12-18-15)22-17(21-14)20-13-8-6-5-7-9-13/h5-12H,3-4H2,1-2H3,(H2,18,19,20,21,22)/b11-10-
InChIKeySHKLUCMYFCYADL-KHPPLWFESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCN(CC)/C=C\c1c2c(nc[nH]2)nc(n1)Nc3ccccc3
OpenEye OEToolkits 2.0.6CCN(CC)C=Cc1c2c(nc[nH]2)nc(n1)Nc3ccccc3
CACTVS 3.385CCN(CC)C=Cc1nc(Nc2ccccc2)nc3nc[nH]c13
CACTVS 3.385CCN(CC)\C=C/c1nc(Nc2ccccc2)nc3nc[nH]c13
FormulaC17 H20 N6
Name6-[(~{Z})-2-(diethylamino)ethenyl]-~{N}-phenyl-7~{H}-purin-2-amine
ChEMBL
DrugBank
ZINCZINC000584905436
PDB chain5m55 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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PDB5m55 Structure-guided design of purine-based probes for selective Nek2 inhibition.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		C22 E87 Y88 C89 G92
Binding residue
(residue number reindexed from 1)		C16 E81 Y82 C83 G86
Annotation score1
Binding affinityMOAD: ic50=0.24uM
PDBbind-CN: -logKd/Ki=6.62,IC50=0.24uM
Enzymatic activity
Catalytic site (original residue number in PDB) K143 A145 N146 D159 T179
Catalytic site (residue number reindexed from 1) K127 A129 N130 D143 T144
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
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Biological Process
External links
PDB RCSB:5m55, PDBe:5m55, PDBj:5m55
PDBsum5m55
PubMed27833088
UniProtP51955|NEK2_HUMAN Serine/threonine-protein kinase Nek2 (Gene Name=NEK2)

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