4HYS

Crystal structure of JNK1 in complex with JIP1 peptide and 4-(4-Indazol-1-yl-pyrimidin-2-ylamino)-cyclohexan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.295 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 1BJClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Development of amino-pyrimidine inhibitors of c-Jun N-terminal kinase (JNK): kinase profiling guided optimization of a 1,2,3-benzotriazole lead.

Palmer, W.S.Alam, M.Arzeno, H.B.Chang, K.C.Dunn, J.P.Goldstein, D.M.Gong, L.Goyal, B.Hermann, J.C.Hogg, J.H.Hsieh, G.Jahangir, A.Janson, C.Jin, S.Ursula Kammlott, R.Kuglstatter, A.Lukacs, C.Michoud, C.Niu, L.Reuter, D.C.Shao, A.Silva, T.Trejo-Martin, T.A.Stein, K.Tan, Y.C.Tivitmahaisoon, P.Tran, P.Wagner, P.Weller, P.Wu, S.Y.

(2013) Bioorg Med Chem Lett 23: 1486-1492

  • DOI: https://doi.org/10.1016/j.bmcl.2012.12.047
  • Primary Citation of Related Structures:  
    4HYS, 4HYU

  • PubMed Abstract: 

    A series of amino-pyrimidines was developed based upon an initial kinase cross-screening hit from a CDK2 program. Kinase profiling and structure-based drug design guided the optimization from the initial 1,2,3-benzotriazole hit to a potent and selective JNK inhibitor, compound 24f (JNK1 and 2 IC(50)=16 and 66 nM, respectively), with bioavailability in rats and suitable for further in vivo pharmacological evaluation.


  • Organizational Affiliation

    Roche Palo Alto, 3431 Hillview Ave., Palo Alto, CA 94304, USA. wyliepalmer@msn.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 8369Homo sapiensMutation(s): 0 
Gene Names: MAPK8hCG_23734
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
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-Jun-amino-terminal kinase-interacting protein 111Homo sapiensMutation(s): 0 
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1BJ
Query on 1BJ

Download Ideal Coordinates CCD File 
C [auth A]trans-4-{[4-(1H-indazol-1-yl)pyrimidin-2-yl]amino}cyclohexanol
C17 H19 N5 O
DPTBYUQHDCZBPL-HDJSIYSDSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.295 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.36α = 90
b = 81.498β = 90
c = 84.471γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 1BJClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description