Structure of PDB 4a4x Chain A Binding Site BS01

Receptor Information
>4a4x 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]
SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQML
VSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGT
KERQYLDEEFVLRVMTQLTLALKECHRRSHRDLKPANVFLDGKQNVKLGD
FGLVGTPYYMSPEQMNRNEKSDIWSLGCLLYELCALMPPFTAFSQKELAG
KIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHH
HHH
Ligand information
Ligand IDJUP
InChIInChI=1S/C28H27F3N4O2S/c1-16(20-6-4-5-7-23(20)28(29,30)31)37-24-12-18(8-9-21(24)27(33)36)22-11-19(13-34-26(22)32)25-10-17(15-38-25)14-35(2)3/h4-13,15-16H,14H2,1-3H3,(H2,32,34)(H2,33,36)/t16-/m1/s1
InChIKeyDNZGEPPZYMAFLN-MRXNPFEDSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC(F)(F)c1ccccc1C(Oc2c(C(=O)N)ccc(c2)c4cc(c3scc(c3)CN(C)C)cnc4N)C
OpenEye OEToolkits 1.9.2CC(c1ccccc1C(F)(F)F)Oc2cc(ccc2C(=O)N)c3cc(cnc3N)c4cc(cs4)CN(C)C
CACTVS 3.385C[CH](Oc1cc(ccc1C(N)=O)c2cc(cnc2N)c3scc(CN(C)C)c3)c4ccccc4C(F)(F)F
OpenEye OEToolkits 1.9.2C[C@H](c1ccccc1C(F)(F)F)Oc2cc(ccc2C(=O)N)c3cc(cnc3N)c4cc(cs4)CN(C)C
CACTVS 3.385C[C@@H](Oc1cc(ccc1C(N)=O)c2cc(cnc2N)c3scc(CN(C)C)c3)c4ccccc4C(F)(F)F
FormulaC28 H27 F3 N4 O2 S
Name4-(2-AMINO-5-{4-[(DIMETHYLAMINO)METHYL]THIOPHEN-2-YL}PYRIDIN-3-YL)-2-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}BENZAMIDE
ChEMBLCHEMBL2042136
DrugBank
ZINCZINC000084655195
PDB chain4a4x 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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PDB4a4x Design of Potent and Selective Hybrid Inhibitors of the Mitotic Kinase Nek2: Structure-Activity Relationship, Structural Biology, and Cellular Activity.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		I14 G15 Y19 C22 V35 M86 Y88 C89 F148 G158 D159 F160
Binding residue
(residue number reindexed from 1)		I12 G13 Y17 C20 V33 M84 Y86 C87 F139 G149 D150 F151
Annotation score1
Binding affinityMOAD: ic50=0.059uM
PDBbind-CN: -logKd/Ki=7.23,IC50=0.059uM
BindingDB: IC50=2700nM
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:4a4x, PDBe:4a4x, PDBj:4a4x
PDBsum4a4x
PubMed22404346
UniProtP51955|NEK2_HUMAN Serine/threonine-protein kinase Nek2 (Gene Name=NEK2)

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