4AN2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 

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:  
    4AN9, 4AN2, 4AN3, 4ANB

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1A301Homo sapiensMutation(s): 3 
Gene Names: MAP2K1MEK1PRKMK1
EC: 2.7.12.2
Find proteins for Q02750 (Homo sapiens)
Explore Q02750 
Go to UniProtKB:  Q02750
NIH Common Fund Data Resources
PHAROS  Q02750
Protein Feature View
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 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EUI
Query on EUI

Download CCD File 
A
[3,4-BIS(FLUORANYL)-2-[(2-FLUORANYL-4-IODANYL-PHENYL)AMINO]PHENYL]-[3-OXIDANYL-3-[(2S)-PIPERIDIN-2-YL]AZETIDIN-1-YL]METHANONE
C21 H21 F3 I N3 O2
BSMCAPRUBJMWDF-KRWDZBQOSA-N
 Ligand Interaction
ACP
Query on ACP

Download CCD File 
A
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EUIIC50 :  0.8999999761581421   nM  PDBBind
EUIIC50:  4.199999809265137   nM  BindingDB
EUIIC50:  0.8999999761581421   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.844α = 90
b = 108.844β = 90
c = 47.71γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

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