Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.95 kDa 
• Atom Count: 3554 
• Modelled Residue Count: 348 
• Deposited Residue Count: 361 
• Unique protein chains: 1

4QTE

Structure of ERK2 in complex with VTX-11e, 4-{2-[(2-CHLORO-4-FLUOROPHENYL)AMINO]-5-METHYLPYRIMIDIN-4-YL}-N-[(1S)-1-(3-CHLOROPHENYL)-2-HYDROXYETHYL]-1H-PYRROLE-2-CARBOXAMIDE

• PDB DOI: 10.2210/pdb4QTE/pdb

• Classification: Transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-07-07 Released: 2014-07-23 
• Deposition Author(s): Chaikuad, A., Savitsky, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.167 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 

Literature

A unique inhibitor binding site in ERK1/2 is associated with slow binding kinetics.

Chaikuad, A., M C Tacconi, E., Zimmer, J., Liang, Y., Gray, N.S., Tarsounas, M., Knapp, S.

(2014) Nat Chem Biol 10: 853-860

• PubMed: 25195011 
• DOI: 10.1038/nchembio.1629
• Primary Citation of Related Structures:  
  4QTA, 4QTB, 4QTC, 4QTD, 4QTE


• PubMed Abstract: 
  

Activation of the ERK pathway is a hallmark of cancer, and targeting of upstream signaling partners led to the development of approved drugs. Recently, SCH772984 has been shown to be a selective and potent ERK1/2 inhibitor. Here we report the structural mechanism for its remarkable selectivity. In ERK1/2, SCH772984 induces a so-far-unknown binding pocket that accommodates the piperazine-phenyl-pyrimidine decoration. This new binding pocket was created by an inactive conformation of the phosphate-binding loop and an outward tilt of helix αC. In contrast, structure determination of SCH772984 with the off-target haspin and JNK1 revealed two canonical but distinct type I binding modes. Notably, the new binding mode with ERK1/2 was associated with slow binding kinetics in vitro as well as in cell-based assay systems. The described binding mode of SCH772984 with ERK1/2 enables the design of a new type of specific kinase inhibitors with prolonged on-target activity.

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Organizational Affiliation: 

1] Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford, UK. [2] Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC, USA. [3] Target Discovery Institute, University of Oxford, Nuffield Department of Medicine Research Building, Oxford, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	361	Homo sapiens	Mutation(s): 0  Gene Names: ERK2, MAPK1, PRKM1, PRKM2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens) Explore P28482  Go to UniProtKB:  P28482
PHAROS:  P28482

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
390	EA [auth A]	4-{2-[(2-chloro-4-fluorophenyl)amino]-5-methylpyrimidin-4-yl}-N-[(1S)-1-(3-chlorophenyl)-2-hydroxyethyl]-1H-pyrrole-2-carboxamide C24 H20 Cl2 F N5 O2 WUTVMXLIGHTZJC-OAQYLSRUSA-N
SO4	AA [auth A], DA [auth A], X [auth A], Y [auth A], Z [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	BA [auth A], CA [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
390	BindingDB:  4QTE	Ki: 2 (nM) from 1 assay(s)
	Binding MOAD:  4QTE	Kd: 84 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.167 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.729	α = 90
b = 96.729	β = 90
c = 95.382	γ = 120

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-07 
• Released Date: 2014-07-23 
Deposition Author(s): Chaikuad, A., Savitsky, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references