4U81

MEK1 Kinase bound to small molecule inhibitor G659


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure based design of novel 6,5 heterobicyclic mitogen-activated protein kinase kinase (MEK) inhibitors leading to the discovery of imidazo[1,5-a] pyrazine G-479.

Robarge, K.D.Lee, W.Eigenbrot, C.Ultsch, M.Wiesmann, C.Heald, R.Price, S.Hewitt, J.Jackson, P.Savy, P.Burton, B.Choo, E.F.Pang, J.Boggs, J.Yang, A.Yang, X.Baumgardner, M.

(2014) Bioorg.Med.Chem.Lett. 24: 4714-4723

  • DOI: 10.1016/j.bmcl.2014.08.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Use of the tools of SBDD including crystallography led to the discovery of novel and potent 6,5 heterobicyclic MEKi's [J. Med. Chem.2012, 55, 4594]. The core change from a 5,6 heterobicycle to a 6,5 heterobicycle was driven by the desire for increase ...

    Use of the tools of SBDD including crystallography led to the discovery of novel and potent 6,5 heterobicyclic MEKi's [J. Med. Chem.2012, 55, 4594]. The core change from a 5,6 heterobicycle to a 6,5 heterobicycle was driven by the desire for increased structural diversity and aided by the co-crystal structure of G-925 [J. Med. Chem.2012, 55, 4594]. The key design feature was the shift of the attachment of the five-membered heterocyclic ring towards the B ring while maintaining the key hydroxamate and anilino pharamcophoric elements in a remarkably similar position as in G-925. From modelling, changing the connection point of the five membered ring heterocycle placed the H-bond accepting nitrogen within a good distance and angle to the Ser212 [J. Med. Chem.2012, 55, 4594]. The resulting novel 6,5 benzoisothiazole MEKi G-155 exhibited improved potency versus aza-benzofurans G-925 and G-963 but was a potent inhibitor of cytochrome P450's 2C9 and 2C19. Lowering the logD by switching to the more polar imidazo[1,5-a] pyridine core significantly diminished 2C9/2C19 inhibition while retaining potency. The imidazo[1,5-a] pyridine G-868 exhibited increased potency versus the starting point for this work (aza-benzofuran G-925) leading to deprioritization of the azabenzofurans. The 6,5-imidazo[1,5-a] pyridine scaffold was further diversified by incorporating a nitrogen at the 7 position to give the imidazo[1,5-a] pyrazine scaffold. The introduction of the C7 nitrogen was driven by the desire to improve metabolic stability by blocking metabolism at the C7 and C8 positions (particularly the HLM stability). It was found that improving on G-868 (later renamed GDC-0623) required combining C7 nitrogen with a diol hydroxamate to give G-479. G-479 with polarity distributed throughout the molecule was improved over G-868 in many aspects.


    Organizational Affiliation

    Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, USA. Electronic address: kir@gene.com.,Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, USA.,Argenta, Discovery Services Charles River, 8-9 Spire Greene Centre, Harlow, Essex CM19 5TR, United Kingdom.,Drug Metabolism and Pharmacokinetics, Genentech Inc., 1 DNA Way, South San Francisco, CA, USA.,Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dual specificity mitogen-activated protein kinase kinase 1
A
341Homo sapiensMutation(s): 0 
Gene Names: MAP2K1 (MEK1, PRKMK1)
EC: 2.7.12.2
Find proteins for Q02750 (Homo sapiens)
Go to Gene View: MAP2K1
Go to UniProtKB:  Q02750
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3EY
Query on 3EY

Download SDF File 
Download CCD File 
A
8-[(4-cyclopropyl-2-fluorophenyl)amino]-N-(2-hydroxyethoxy)imidazo[1,5-a]pyridine-7-carboxamide
C19 H19 F N4 O3
SXXAGUWDTVENNX-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

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Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 82.083α = 90.00
b = 82.083β = 90.00
c = 129.480γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Database references