4IZY

Crystal structure of JNK1 in complex with JIP1 peptide and 4-{4-[4-(4-Methanesulfonyl-piperidin-1-yl)-indol-1-yl]-pyrimidin-2-ylamino}-cyclohexan

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

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Ligand Structure Quality Assessment 


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Literature

Development of indole/indazole-aminopyrimidines as inhibitors of c-Jun N-terminal kinase (JNK): optimization for JNK potency and physicochemical properties.

Gong, L., Han, X., Silva, T., Tan, Y.C., Goyal, B., Tivitmahaisoon, P., Trejo, A., Palmer, W., Hogg, H., Jahagir, A., Alam, M., Wagner, P., Stein, K., Filonova, L., Loe, B., Makra, F., Rotstein, D., Rapatova, L., Dunn, J., Zuo, F., Dal Porto, J., Wong, B., Jin, S., Chang, A., Tran, P., Hsieh, G., Niu, L., Shao, A., Reuter, D., Hermann, J., Kuglstatter, A., Goldstein, D.

(2013) Bioorg Med Chem Lett 23: 3565-3569

  • DOI: 10.1016/j.bmcl.2013.04.029
  • Primary Citation of Related Structures:  
    4IZY

  • PubMed Abstract: 

    • A novel series of indole/indazole-aminopyrimidines was designed and synthesized with an aim to achieve optimal potency and selectivity for the c-Jun kinase family or JNKs. Structure guided design was used to optimize the series resulting in a significant potency improvement ...

    A novel series of indole/indazole-aminopyrimidines was designed and synthesized with an aim to achieve optimal potency and selectivity for the c-Jun kinase family or JNKs. Structure guided design was used to optimize the series resulting in a significant potency improvement. The best compound (17) has IC50 of 3 nM for JNK1 and 20 nM for JNK2, with greater than 40-fold selectivity against other kinases with good physicochemical and pharmacokinetic properties.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Roche Palo Alto, Palo Alto, CA 94304, USA. leyi.gong@sri.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 8A369Homo sapiensMutation(s): 0 
Gene Names: MAPK8, hCG_23734, JNK1, PRKM8, SAPK1, SAPK1C
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P45983 (Homo sapiens)
Explore P45983 
Go to UniProtKB:  P45983
PHAROS:  P45983
GTEx:  ENSG00000107643 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45983
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
C-Jun-amino-terminal kinase-interacting protein 1B11Homo sapiensMutation(s): 0 
Gene Names: MAPK8IP1, IB1, JIP1, PRKM8IP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQF2 (Homo sapiens)
Explore Q9UQF2 
Go to UniProtKB:  Q9UQF2
PHAROS:  Q9UQF2
GTEx:  ENSG00000121653 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQF2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1J2
Query on 1J2
Download Ideal Coordinates CCD File 
C [auth A]trans-4-[(4-{4-[4-(methylsulfonyl)piperidin-1-yl]-1H-indol-1-yl}pyrimidin-2-yl)amino]cyclohexanol
C24 H31 N5 O3 S
VUQJMYORHRVTLM-IYARVYRRSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1J2 BindingDB:  4IZY Kd: 0.14 (nM) from 1 assay(s)
IC50: min: 3, max: 240 (nM) from 5 assay(s)
Binding MOAD:  4IZY IC50: 3 (nM) from 1 assay(s)
PDBBind:  4IZY IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.426α = 90
b = 82.371β = 90
c = 82.027γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release