4HYU

Crystal structure of JNK1 in complex with JIP1 peptide and 4-{4-[4-(3-Methanesulfonyl-propoxy)-indazol-1-yl]-pyrimidin-2-ylamino}-cyclohexan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.0 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 8A369Homo sapiensMutation(s): 0 
Gene Names: MAPK8hCG_23734JNK1PRKM8SAPK1SAPK1C
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: MAPK8IP1IB1JIP1PRKM8IP
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
1BK
Query on 1BK

Download Ideal Coordinates CCD File 
C [auth A]trans-4-[(4-{4-[3-(methylsulfonyl)propoxy]-1H-indazol-1-yl}pyrimidin-2-yl)amino]cyclohexanol
C21 H27 N5 O4 S
QTUUSRHXDAHSAU-WKILWMFISA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1BK BindingDB:  4HYU IC50: min: 6.2, max: 1000 (nM) from 3 assay(s)
PDBBind:  4HYU IC50: 6.2 (nM) from 1 assay(s)
Binding MOAD:  4HYU IC50: 6.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.438α = 90
b = 81.769β = 90
c = 82.502γ = 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 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release