4Z9L

THE STRUCTURE OF JNK3 IN COMPLEX WITH AN IMIDAZOLE-PYRIMIDINE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

  • Primary Citation of Related Structures:  

  • 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 neurolo ...

    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.


    Related Citations: 
    • Achieving High Quality Ligand Chemistry in Protein-Ligand Crystal Structures for Drug Design
      Smart, O.S.,Bricogne, G.
      (2015) Multifaceted Roles Of Crystallography In Modern Drug Discovery --: 165


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 10
A
364Homo sapiensMutation(s): 0 
Gene Names: MAPK10 (JNK3, JNK3A, PRKM10, SAPK1B)
EC: 2.7.11.24
Find proteins for P53779 (Homo sapiens)
Go to Gene View: MAPK10
Go to UniProtKB:  P53779
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
880
Query on 880

Download SDF File 
Download CCD File 
A
CYCLOHEXYL-{4-[5-(3,4-DICHLOROPHENYL)-2-PIPERIDIN-4-YL-3-PROPYL-3H-IMIDAZOL-4-YL]-PYRIMIDIN-2-YL}AMINE
C27 H34 Cl2 N6
UQFRSHRWRKYNDE-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
880IC50: 1.6 - 2 nM (100) BINDINGDB
880IC50: 1.6 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.951α = 90.00
b = 71.525β = 90.00
c = 106.000γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTERrefinement
Cootmodel building
CNXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release