3V6S

Discovery of potent and selective covalent inhibitors of JNK

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

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Literature

Discovery of potent and selective covalent inhibitors of JNK.

Zhang, T., Inesta-Vaquera, F., Niepel, M., Zhang, J., Ficarro, S.B., Machleidt, T., Xie, T., Marto, J.A., Kim, N., Sim, T., Laughlin, J.D., Park, H., LoGrasso, P.V., Patricelli, M., Nomanbhoy, T.K., Sorger, P.K., Alessi, D.R., Gray, N.S.

(2012) Chem Biol 19: 140-154

  • DOI: 10.1016/j.chembiol.2011.11.010
  • Primary Citation of Related Structures:  
    3V6R, 3V6S

  • PubMed Abstract: 

    • The mitogen-activated kinases JNK1/2/3 are key enzymes in signaling modules that transduce and integrate extracellular stimuli into coordinated cellular response. Here, we report the discovery of irreversible inhibitors of JNK1/2/3. We describe two JNK3 cocrystal structures at 2 ...

    The mitogen-activated kinases JNK1/2/3 are key enzymes in signaling modules that transduce and integrate extracellular stimuli into coordinated cellular response. Here, we report the discovery of irreversible inhibitors of JNK1/2/3. We describe two JNK3 cocrystal structures at 2.60 and 2.97 Å resolution that show the compounds form covalent bonds with a conserved cysteine residue. JNK-IN-8 is a selective JNK inhibitor that inhibits phosphorylation of c-Jun, a direct substrate of JNK, in cells exposed to submicromolar drug in a manner that depends on covalent modification of the conserved cysteine residue. Extensive biochemical, cellular, and pathway-based profiling establish the selectivity of JNK-IN-8 for JNK and suggests that the compound will be broadly useful as a pharmacological probe of JNK-dependent signal transduction. Potential lead compounds have also been identified for kinases, including IRAK1, PIK3C3, PIP4K2C, and PIP5K3.

    Organizational Affiliation: 

    Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10A, B364Homo sapiensMutation(s): 0 
Gene Names: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
PHAROS:  P53779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53779
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0F0
Query on 0F0
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		3-{[4-(dimethylamino)butanoyl]amino}-N-(4-{[4-(pyridin-3-yl)pyrimidin-2-yl]amino}phenyl)benzamide
C28 H29 N7 O2
QHAGMZSIDYTUPB-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0F0 PDBBind:  3V6S IC50: 0.75 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.491α = 90
b = 156.262β = 90
c = 43.884γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references