3NPC

Crystal structure of JNK2 complexed with BIRB796

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

X-ray crystal structure of JNK2 complexed with the p38alpha inhibitor BIRB796: Insights into the rational design of DFG-out binding MAP kinase inhibitors.

Kuglstatter, A., Ghate, M., Tsing, S., Villasenor, A.G., Shaw, D., Barnett, J.W., Browner, M.F.

(2010) Bioorg.Med.Chem.Lett. 20: 5217-5220

  • DOI: 10.1016/j.bmcl.2010.06.157

  • PubMed Abstract: 

    • JNK2 and p38alpha are closely related mitogen-activated protein kinases that regulate various cellular activities and are considered drug targets for inflammatory diseases. We have determined the X-ray crystal structure of the clinical phase II p38al ...

    JNK2 and p38alpha are closely related mitogen-activated protein kinases that regulate various cellular activities and are considered drug targets for inflammatory diseases. We have determined the X-ray crystal structure of the clinical phase II p38alpha inhibitor BIRB796 bound to its off-target JNK2. This shows for the first time a JNK subfamily member in the DFG-out conformation. The fully resolved activation loop reveals that BIRB796 inhibits JNK2 activation by stabilizing the loop in a position that does not allow its phosphorylation by upstream kinases. The structure suggests that substituents at the BIRB796 morpholino group and modifications of the t-butyl moiety should further increase the p38alpha to JNK2 potency ratio. For the design of selective DFG-out binding JNK2 inhibitors, the binding pocket of the BIRB796 tolyl group may have the best potential.

    Organizational Affiliation: 

    Roche Palo Alto, Palo Alto, CA 94304, USA. andreas.kuglstatter@roche.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 9
A, B
364Homo sapiensMutation(s): 8 
Gene Names: MAPK9 (JNK2, PRKM9, SAPK1A)
EC: 2.7.11.24
Find proteins for P45984 (Homo sapiens)
Go to Gene View: MAPK9
Go to UniProtKB:  P45984
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B96
Query on B96
Download SDF File 
Download CCD File 
A, B
1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA
C31 H37 N5 O3
MVCOAUNKQVWQHZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B96Kd: 4.6 - 7300 nM (97) BINDINGDB
B96IC50: 6 - >10000 nM (97) BINDINGDB
B96Kd: 4.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.170α = 90.00
b = 92.339β = 90.00
c = 112.109γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
ADSCdata collection
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance