6G9M

Fragment-based discovery of a highly potent, orally bioavailable inhibitor which modulates the phosphorylation and catalytic activity of ERK1/2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Fragment-Based Discovery of a Potent, Orally Bioavailable Inhibitor That Modulates the Phosphorylation and Catalytic Activity of ERK1/2.

Heightman, T.D.Berdini, V.Braithwaite, H.Buck, I.M.Cassidy, M.Castro, J.Courtin, A.Day, J.E.H.East, C.Fazal, L.Graham, B.Griffiths-Jones, C.M.Lyons, J.F.Martins, V.Muench, S.Munck, J.M.Norton, D.O'Reilly, M.Palmer, N.Pathuri, P.Reader, M.Rees, D.C.Rich, S.J.Richardson, C.Saini, H.Thompson, N.T.Wallis, N.G.Walton, H.Wilsher, N.E.Woolford, A.J.Cooke, M.Cousin, D.Onions, S.Shannon, J.Watts, J.Murray, C.W.

(2018) J Med Chem 61: 4978-4992

  • DOI: 10.1021/acs.jmedchem.8b00421
  • Primary Citation of Related Structures:  
    6G9A, 6G9D, 6G8X, 6G91, 6G93, 6G92, 6G97, 6G9H, 6G9K, 6G9J, 6G9M, 6G9N, 6GDM, 6GE0, 6GDQ

  • PubMed Abstract: 
  • Aberrant activation of the MAPK pathway drives cell proliferation in multiple cancers. Inhibitors of BRAF and MEK kinases are approved for the treatment of BRAF mutant melanoma, but resistance frequently emerges, often mediated by increased signaling through ERK1/2 ...

    Aberrant activation of the MAPK pathway drives cell proliferation in multiple cancers. Inhibitors of BRAF and MEK kinases are approved for the treatment of BRAF mutant melanoma, but resistance frequently emerges, often mediated by increased signaling through ERK1/2. Here, we describe the fragment-based generation of ERK1/2 inhibitors that block catalytic phosphorylation of downstream substrates such as RSK but also modulate phosphorylation of ERK1/2 by MEK without directly inhibiting MEK. X-ray crystallographic and biophysical fragment screening followed by structure-guided optimization and growth from the hinge into a pocket proximal to the C-α helix afforded highly potent ERK1/2 inhibitors with excellent kinome selectivity. In BRAF mutant cells, the lead compound suppresses pRSK and pERK levels and inhibits proliferation at low nanomolar concentrations. The lead exhibits tumor regression upon oral dosing in BRAF mutant xenograft models, providing a promising basis for further optimization toward clinical pERK1/2 modulating ERK1/2 inhibitors.


    Organizational Affiliation

    Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 1A368Homo sapiensMutation(s): 0 
Gene Names: MAPK1ERK2PRKM1PRKM2
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens)
Explore P28482 
Go to UniProtKB:  P28482
PHAROS:  P28482
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ESW (Subject of Investigation/LOI)
Query on ESW

Download Ideal Coordinates CCD File 
E [auth A]2-[5-[5-chloranyl-2-(oxan-4-ylamino)pyrimidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]-~{N}-(2-phenylpropan-2-yl)ethanamide
C28 H30 Cl N5 O3
OBEQPUMSPDLFGN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
AL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Binding Affinity Annotations 
IDSourceBinding Affinity
ESW BindingDB:  6G9M IC50: 7.9 (nM) from 1 assay(s)
Binding MOAD:  6G9M IC50: 7.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.808α = 90
b = 70.843β = 109.65
c = 60.375γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-04-11 
  • Released Date: 2018-05-30 
  • Deposition Author(s): O'Reilly, M.

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.2: 2018-06-27
    Changes: Data collection, Database references