Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.50 kDa 
• Atom Count: 3016 
• Modelled Residue Count: 350 
• Deposited Residue Count: 364 
• Unique protein chains: 1

3ERK

THE COMPLEX STRUCTURE OF THE MAP KINASE ERK2/SB220025

• PDB DOI: 10.2210/pdb3ERK/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1998-07-09 Released: 1999-07-22 
• Deposition Author(s): Wang, Z., Canagarajah, B., Boehm, J.C., Cobb, M.H., Young, P.R., Abdel-Meguid, S., Adams, J.L., Goldsmith, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.262 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Literature

Structural basis of inhibitor selectivity in MAP kinases.

Wang, Z., Canagarajah, B.J., Boehm, J.C., Kassisa, S., Cobb, M.H., Young, P.R., Abdel-Meguid, S., Adams, J.L., Goldsmith, E.J.

(1998) Structure 6: 1117-1128

• PubMed: 9753691 
• DOI: 10.1016/s0969-2126(98)00113-0
• Primary Citation of Related Structures:  
  1A9U, 1BL6, 1BL7, 1BMK, 3ERK, 4ERK


• PubMed Abstract: 
  

The mitogen-activated protein (MAP) kinases are important signaling molecules that participate in diverse cellular events and are potential targets for intervention in inflammation, cancer, and other diseases. The MAP kinase p38 is responsive to environmental stresses and is involved in the production of cytokines during inflammation. In contrast, the activation of the MAP kinase ERK2 (extracellular-signal-regulated kinase 2) leads to cellular differentiation or proliferation. The anti-inflammatory agent pyridinylimidazole and its analogs (SB [SmithKline Beecham] compounds) are highly potent and selective inhibitors of p38, but not of the closely-related ERK2, or other serine/threonine kinases. Although these compounds are known to bind to the ATP-binding site, the origin of the inhibitory specificity toward p38 is not clear.

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Organizational Affiliation: 

Department of Biochemistry The University of Texas Southwestern Medical Center at Dallas 5323 Harry Hines Boulevard, Dallas, TX 75235, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXTRACELLULAR REGULATED KINASE 2	A	364	Rattus norvegicus	Mutation(s): 0  Gene Names: Mapk1, Erk2, Mapk, Prkm1 EC: 2.7.1 (PDB Primary Data), 2.7.11.24 (UniProt)
UniProt
Find proteins for P63086 (Rattus norvegicus) Explore P63086  Go to UniProtKB:  P63086

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SB4	B [auth A]	4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE C18 H19 F N6 VSPFURGQAYMVAN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SB4	Binding MOAD:  3ERK	IC50: 1.80e+4 (nM) from 1 assay(s)
	PDBBind:  3ERK	IC50: 1.80e+4 (nM) from 1 assay(s)
	BindingDB:  3ERK	IC50: min: 1.80e+4, max: 1.90e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.262 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.85	α = 90
b = 70	β = 109.2
c = 60.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-07-09 
• Released Date: 1999-07-22 
Deposition Author(s): Wang, Z., Canagarajah, B., Boehm, J.C., Cobb, M.H., Young, P.R., Abdel-Meguid, S., Adams, J.L., Goldsmith, E.J.

Revision History  

• Version 1.0: 1999-07-22
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance