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 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1107/S2059798316004502
  • Primary Citation of Related Structures:  
    4ZSG, 4ZSJ, 4ZSL, 5BYY, 5BYZ

  • 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 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

    Chemistry Innovation Centre, Discovery Sciences, AstraZeneca R&D Mölndal, 431 83 Mölndal, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 7346Homo sapiensMutation(s): 0 
Gene Names: MAPK7BMK1ERK5PRKM7
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q13164 (Homo sapiens)
Explore Q13164 
Go to UniProtKB:  Q13164
PHAROS:  Q13164
GTEx:  ENSG00000166484 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13164
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4WG
Query on 4WG

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
4WG BindingDB:  5BYY Kd: 80 (nM) from 1 assay(s)
IC50: min: 200, max: 300 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.791α = 90
b = 92.791β = 90
c = 107.321γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references