6HKN

Crystal structure of Compound 35 with ERK5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery and Characterization of the Potent and Highly Selective (Piperidin-4-yl)pyrido[3,2- d]pyrimidine Based in Vitro Probe BAY-885 for the Kinase ERK5.

Nguyen, D.Lemos, C.Wortmann, L.Eis, K.Holton, S.J.Boemer, U.Moosmayer, D.Eberspaecher, U.Weiske, J.Lechner, C.Prechtl, S.Suelzle, D.Siegel, F.Prinz, F.Lesche, R.Nicke, B.Nowak-Reppel, K.Himmel, H.Mumberg, D.von Nussbaum, F.Nising, C.F.Bauser, M.Haegebarth, A.

(2019) J Med Chem 62: 928-940

  • DOI: 10.1021/acs.jmedchem.8b01606
  • Primary Citation of Related Structures:  
    6HKN, 6HKM

  • PubMed Abstract: 
  • The availability of a chemical probe to study the role of a specific domain of a protein in a concentration- and time-dependent manner is of high value. Herein, we report the identification of a highly potent and selective ERK5 inhibitor BAY-885 by high-throughput screening and subsequent structure-based optimization ...

    The availability of a chemical probe to study the role of a specific domain of a protein in a concentration- and time-dependent manner is of high value. Herein, we report the identification of a highly potent and selective ERK5 inhibitor BAY-885 by high-throughput screening and subsequent structure-based optimization. ERK5 is a key integrator of cellular signal transduction, and it has been shown to play a role in various cellular processes such as proliferation, differentiation, apoptosis, and cell survival. We could demonstrate that inhibition of ERK5 kinase and transcriptional activity with a small molecule did not translate into antiproliferative activity in different relevant cell models, which is in contrast to the results obtained by RNAi technology.


    Organizational Affiliation

    Research & Development, Pharmaceuticals , Bayer AG , 13353 Berlin , Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 7A340Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G9E (Subject of Investigation/LOI)
Query on G9E

Download Ideal Coordinates CCD File 
B [auth A][2-azanyl-4-(trifluoromethyloxy)phenyl]-[4-(7-methoxyquinazolin-4-yl)piperidin-1-yl]methanone
C22 H21 F3 N4 O3
UCMVZMXGBOBQEZ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
G9E Binding MOAD:  6HKN IC50: 51 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.488α = 90
b = 92.488β = 90
c = 113.585γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release