1PMN

Crystal structure of JNK3 in complex with an imidazole-pyrimidine inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

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This is version 1.3 of the entry. See complete history. 


Literature

The structure of JNK3 in complex with small molecule inhibitors: structural basis for potency and selectivity

Scapin, G., Patel, S.B., Lisnock, J., Becker, J.W., LoGrasso, P.V.

(2003) Chem Biol 10: 705-712

  • DOI: 10.1016/s1074-5521(03)00159-5
  • Primary Citation of Related Structures:  
    1PMN, 1PMU, 1PMV, 4Z9L

  • PubMed Abstract: 

    • The c-Jun terminal kinases (JNKs) are members of the mitogen-activated protein (MAP) kinase family and regulate signal transduction in response to environmental stress. Activation of JNK3, a neuronal-specific isoform, has been associated with neurological damage, and as such, JNK3 may represent an attractive target for the treatment of neurological disorders ...

    The c-Jun terminal kinases (JNKs) are members of the mitogen-activated protein (MAP) kinase family and regulate signal transduction in response to environmental stress. Activation of JNK3, a neuronal-specific isoform, has been associated with neurological damage, and as such, JNK3 may represent an attractive target for the treatment of neurological disorders. The MAP kinases share between 50% and 80% sequence identity. In order to obtain efficacious and safe compounds, it is necessary to address the issues of potency and selectivity. We report here four crystal structures of JNK3 in complex with three different classes of inhibitors. These structures provide a clear picture of the interactions that each class of compound made with the kinase. Knowledge of the atomic interactions involved in these diverse binding modes provides a platform for structure-guided modification of these compounds, or the de novo design of novel inhibitors that could satisfy the need for potency and selectivity.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Merck Research Laboratories, P.O. Box 2000, Rahway, NJ 07065, USA. giovanna_scapin@merck.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10A364Homo sapiensMutation(s): 0 
Gene Names: MK10_HUMAN, MAPK10, JNK3, JNK3A, PRKM10, SAPK1B
EC: 2.7.1 (PDB Primary Data), 2.7.11.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
PHAROS:  P53779
GTEx:  ENSG00000109339 
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
984
Query on 984
Download Ideal Coordinates CCD File 
B [auth A]CYCLOPROPYL-{4-[5-(3,4-DICHLOROPHENYL)-2-[(1-METHYL)-PIPERIDIN]-4-YL-3-PROPYL-3H-IMIDAZOL-4-YL]-PYRIMIDIN-2-YL}AMINE
C25 H30 Cl2 N6
XCTKFTOEAKJMII-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
984 PDBBind:  1PMN IC50: 7.1 (nM) from 1 assay(s)
BindingDB:  1PMN IC50: min: 1.6, max: 7.1 (nM) from 2 assay(s)
Binding MOAD:  1PMN IC50: 7.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.075α = 90
b = 71.341β = 90
c = 107.174γ = 90
Software Package:
Software NamePurpose
X-GENdata scaling
X-GENdata reduction
CNXrefinement
CNXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description