4AN3

Crystal structures of human MEK1 with carboxamide-based allosteric inhibitor XL518 (GDC-0973), or related analogs.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Novel Carboxamide-Based Allosteric Mek Inhibitors: Discovery and Optimization Efforts Toward Xl518 (Gdc-0973)

Rice, K.D.Aay, N.Anand, N.K.Blazey, C.M.Bowles, O.J.Bussenius, J.Costanzo, S.Curtis, J.K.Defina, S.C.Dubenko, L.Engst, S.Joshi, A.A.Kennedy, A.R.Kim, A.I.Koltun, E.S.Lougheed, J.C.Manalo, J.C.L.Martini, J.F.Nuss, J.M.Peto, C.J.Tsang, T.H.Yu, P.Johnston, S.

(2012) Acs Med.Chem.Lett. 3: 416

  • DOI: 10.1021/ml300049d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ERK/MAP kinase cascade is a key mechanism subject to dysregulation in cancer and is constitutively activated or highly upregulated in many tumor types. Mutations associated with upstream pathway components RAS and Raf occur frequently and contrib ...

    The ERK/MAP kinase cascade is a key mechanism subject to dysregulation in cancer and is constitutively activated or highly upregulated in many tumor types. Mutations associated with upstream pathway components RAS and Raf occur frequently and contribute to the oncogenic phenotype through activation of MEK and then ERK. Inhibitors of MEK have been shown to effectively block upregulated ERK/MAPK signaling in a range of cancer cell lines and have further demonstrated early evidence of efficacy in the clinic for the treatment of cancer. Guided by structural insight, a strategy aimed at the identification of an optimal diphenylamine-based MEK inhibitor with an improved metabolism and safety profile versus PD-0325901 led to the discovery of development candidate 1-({3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl}carbonyl)-3-[(2S)-piperidin-2-yl]azetidin-3-ol (XL518, GDC-0973) (1). XL518 exhibits robust in vitro and in vivo potency and efficacy in preclinical models with sustained duration of action and is currently in early stage clinical trials.


    Organizational Affiliation

    Exelixis Inc. , 210 East Grand Avenue, South San Francisco, California 94080, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1
A
301Homo sapiensMutation(s): 3 
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
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
5Y0
Query on 5Y0

Download SDF File 
Download CCD File 
A
N-[(2S)-2,3-bis(oxidanyl)propoxy]-3,4-bis(fluoranyl)-2-[(2-fluoranyl-4-iodanyl-phenyl)amino]benzamide
N-(2,3-DIHYDROXYPROPOXY)-3,4-DIFLUORO-2-[(2-FLUORO-4-IODOPHENYL)AMINO]BENZAMIDE
C16 H14 F3 I N2 O4
SUDAHWBOROXANE-VIFPVBQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5Y0IC50: 0.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 108.659α = 90.00
b = 108.659β = 90.00
c = 50.113γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2014-06-18
    Type: Database references