Structure of PDB 5ekn Chain A Binding Site BS01

Receptor Information
>5ekn Chain A (length=336) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLIRKKGFYKQDVNKTAWELPKTYVSPTHVGSGAYGSVCSAIDKRSGEKV
AIKKLSRPFQSEIFAKRAYRELLLLKHMQHENVIGLLDVFTPASSLRNFY
DFYLVMPFMQTDLQKIMGMEFSEEKIQYLVYQMLKGLKYIHSAGVVHRDL
KPGNLAVNEDCELKILDFVTRWYRAPEVILSWMHYNQTVDIWSVGCIMAE
MLTGKTLFKGKDYLDQLTQILKVTGVPGTEFVQKLNDKAAKSYIQSLPQT
PRKDFTQLFPRASPQAADLLEKMLELDVDKRLTAAQALTHPFFEPFRDPE
EETEAQQPFDDSLEHEKLTVDEWKQHIYKEIVNFSP
Ligand information
Ligand IDN58
InChIInChI=1S/C20H23N5OS/c1-20(2,3)17-13-18(25(4)24-17)23-19(26)22-14-5-7-15(8-6-14)27-16-9-11-21-12-10-16/h5-13H,1-4H3,(H2,22,23,26)
InChIKeyFDHKHZIFBOZGKU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(Nc1cc(nn1C)C(C)(C)C)Nc3ccc(Sc2ccncc2)cc3
CACTVS 3.385Cn1nc(cc1NC(=O)Nc2ccc(Sc3ccncc3)cc2)C(C)(C)C
OpenEye OEToolkits 1.7.6CC(C)(C)c1cc(n(n1)C)NC(=O)Nc2ccc(cc2)Sc3ccncc3
FormulaC20 H23 N5 O S
Name1-(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)-3-[4-(pyridin-4-ylsulfanyl)phenyl]urea
ChEMBLCHEMBL41723
DrugBank
ZINCZINC000013442545
PDB chain5ekn Chain A Residue 401 [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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PDB5ekn First comprehensive structural and biophysical analysis of MAPK13 inhibitors targeting DFG-in and DFG-out binding modes.
Resolution2.594 Å
Binding residue
(original residue number in PDB)		V39 A52 E72 M107 P108 F109 M110 D168 F169
Binding residue
(residue number reindexed from 1)		V38 A51 E71 M106 P107 F108 M109 D167 F168
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.72,Kd=1.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) D150 K152 N155 D168 T185
Catalytic site (residue number reindexed from 1) D149 K151 N154 D167 T170
Enzyme Commision number 2.7.11.24: mitogen-activated protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004707 MAP kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0000165 MAPK cascade
GO:0006468 protein phosphorylation
GO:0006970 response to osmotic stress
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0032755 positive regulation of interleukin-6 production
GO:0033554 cellular response to stress
GO:0034644 cellular response to UV
GO:0035556 intracellular signal transduction
GO:0050729 positive regulation of inflammatory response
GO:0051403 stress-activated MAPK cascade
GO:0070301 cellular response to hydrogen peroxide
GO:0071347 cellular response to interleukin-1
GO:0072709 cellular response to sorbitol
GO:0072740 cellular response to anisomycin
GO:1903936 cellular response to sodium arsenite
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ekn, PDBe:5ekn, PDBj:5ekn
PDBsum5ekn
PubMed27369736
UniProtO15264|MK13_HUMAN Mitogen-activated protein kinase 13 (Gene Name=MAPK13)

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