Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42487.09 
• Atom Count: 2807 
• Residue Count: 364 
• Unique protein chains: 1

1PMN

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

• DOI: 10.2210/pdb1PMN/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2003-06-11 Released: 2003-09-09 
• Deposition Author(s): Scapin, G., Patel, S.B., Lisnock, J., Becker, J.W., LoGrasso, P.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.266 
• R-Value Work: 0.228 

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

• PubMed: 12954329 
• Primary Citation of Related Structures:  
  4Z9L, 1PMV, 1PMU, 1PMQ


• 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 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.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, P.O. Box 2000, Rahway, NJ 07065, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Mitogen-activated protein kinase 10	A	364	Homo sapiens	Mutation(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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
984	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
984	IC50: 1.6 - 7.1 nM (100) BINDINGDB
984	IC50: 7.1 nM BINDINGMOAD
984	IC50: 7.1 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.266 
• R-Value Work: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 53.075	α = 90.00
b = 71.341	β = 90.00
c = 107.174	γ = 90.00

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
CNX	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-11 
• Released Date: 2003-09-09 
• Deposition Author(s): Scapin, G., Patel, S.B., Lisnock, J., Becker, J.W., LoGrasso, P.V.

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