4B99

Crystal Structure of MAPK7 (ERK5) with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-Ray Crystal Structure of Erk5 (Mapk7) in Complex with a Specific Inhibitor.

Elkins, J.M.Wang, J.Deng, X.Pattison, M.J.Arthur, S.Erazo, T.Gomez, N.Lizcano, J.M.Gray, N.S.Knapp, S.

(2013) J.Med.Chem. 56: 4413

  • DOI: 10.1021/jm4000837

  • PubMed Abstract: 
  • The protein kinase ERK5 (MAPK7) is an emerging drug target for a variety of indications, in particular for cancer where it plays a key role mediating cell proliferation, survival, epithelial-mesenchymal transition, and angiogenesis. To date, no three ...

    The protein kinase ERK5 (MAPK7) is an emerging drug target for a variety of indications, in particular for cancer where it plays a key role mediating cell proliferation, survival, epithelial-mesenchymal transition, and angiogenesis. To date, no three-dimensional structure has been published that would allow rational design of inhibitors. To address this, we determined the X-ray crystal structure of the human ERK5 kinase domain in complex with a highly specific benzo[e]pyrimido[5,4-b]diazepine-6(11H)-one inhibitor. The structure reveals that specific residue differences in the ATP-binding site, compared to the related ERKs p38s and JNKs, allow for the development of ERK5-specific inhibitors. The selectivity of previously observed ERK5 inhibitors can also be rationalized using this structure, which provides a template for future development of inhibitors with potential for treatment of disease.


    Organizational Affiliation

    Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MITOGEN-ACTIVATED PROTEIN KINASE 7
A
398Homo sapiensMutation(s): 0 
Gene Names: MAPK7 (BMK1, ERK5, PRKM7)
EC: 2.7.11.24
Find proteins for Q13164 (Homo sapiens)
Go to Gene View: MAPK7
Go to UniProtKB:  Q13164
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R4L
Query on R4L

Download SDF File 
Download CCD File 
A
11-cyclopentyl-2-[[2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl-phenyl]amino]-5-methyl-pyrimido[4,5-b][1,4]benzodiazepin-6-one
C35 H44 N8 O3
OXSKLFUMHBJZNS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.222 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.150α = 90.00
b = 95.150β = 90.00
c = 119.450γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references
  • Version 1.2: 2013-06-26
    Type: Database references
  • Version 1.3: 2018-01-24
    Type: Structure summary