1PMU

The crystal structure of JNK3 in complex with a phenantroline inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


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

  • Primary Citation of Related Structures:  1PMN, 1PMQ, 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 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.


    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 sapiensGene 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
9HP
Query on 9HP

Download SDF File 
Download CCD File 
A
9-(4-HYDROXYPHENYL)-2,7-PHENANTHROLINE
C18 H12 N2 O
IUSSGTWHFMSCOY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9HPIC50: 590 nM (100) BINDINGDB
9HPIC50: 590 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.401α = 90.00
b = 62.377β = 90.00
c = 98.119γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
X-GENdata scaling
CNXrefinement
X-GENdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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