5BYY

ERK5 IN COMPLEX WITH SMALL MOLECULE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a novel allosteric inhibitor-binding site in ERK5: comparison with the canonical kinase hinge ATP-binding site.

Chen, H.Tucker, J.Wang, X.Gavine, P.R.Phillips, C.Augustin, M.A.Schreiner, P.Steinbacher, S.Preston, M.Ogg, D.

(2016) Acta Crystallogr D Struct Biol 72: 682-693

  • DOI: 10.1107/S2059798316004502
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • MAP kinases act as an integration point for multiple biochemical signals and are involved in a wide variety of cellular processes such as proliferation, differentiation, regulation of transcription and development. As a member of the MAP kinase famil ...

    MAP kinases act as an integration point for multiple biochemical signals and are involved in a wide variety of cellular processes such as proliferation, differentiation, regulation of transcription and development. As a member of the MAP kinase family, ERK5 (MAPK7) is involved in the downstream signalling pathways of various cell-surface receptors, including receptor tyrosine kinases and G protein-coupled receptors. In the current study, five structures of the ERK5 kinase domain co-crystallized with ERK5 inhibitors are reported. Interestingly, three of the compounds bind at a novel allosteric binding site in ERK5, while the other two bind at the typical ATP-binding site. Binding of inhibitors at the allosteric site is accompanied by displacement of the P-loop into the ATP-binding site and is shown to be ATP-competitive in an enzymatic assay of ERK5 kinase activity. Kinase selectivity data show that the most potent allosteric inhibitor exhibits superior kinase selectivity compared with the two inhibitors that bind at the canonical ATP-binding site. An analysis of these structures and comparison with both a previously published ERK5-inhibitor complex structure (PDB entry 4b99) and the structures of three other kinases (CDK2, ITK and MEK) in complex with allosteric inhibitors are presented.


    Organizational Affiliation

    Innovation Centre China, AstraZeneca Asia and Emerging Markets iMed, Shanghai 201203, People's Republic of China.,Chemistry Innovation Centre, Discovery Sciences, AstraZeneca R&D Mölndal, 431 83 Mölndal, Sweden.,Structure and Biophysics, Discovery Sciences, AstraZeneca R&D Alderley Park, Macclesfield SK10 4TG, England.,Proteros biostructures GmbH, Bunsenstrasse 7a, 82152 Martinsried, Germany.,Screening Sciences, Discovery Sciences, AstraZeneca R&D Alderley Park, Macclesfield SK10 4TG, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 7
A
346Homo 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
4WG
Query on 4WG

Download SDF File 
Download CCD File 
A
2-{[2-ethoxy-4-(4-hydroxypiperidin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one
C26 H30 N6 O3
QAPAJIZPZGWAND-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.791α = 90.00
b = 92.791β = 90.00
c = 107.321γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XSCALEdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-11
    Type: Database references