Mitogen-activated protein kinase kinase 1 (MEK1) in complex with CH4858061 and MgATP

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.268 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Design and synthesis of novel allosteric MEK inhibitor CH4987655 as an orally available anticancer agent.

Isshiki, Y.Kohchi, Y.Iikura, H.Matsubara, Y.Asoh, K.Murata, T.Kohchi, M.Mizuguchi, E.Tsujii, S.Hattori, K.Miura, T.Yoshimura, Y.Aida, S.Miwa, M.Saitoh, R.Murao, N.Okabe, H.Belunis, C.Janson, C.Lukacs, C.Schuck, V.Shimma, N.

(2011) Bioorg Med Chem Lett 21: 1795-1801

  • DOI: https://doi.org/10.1016/j.bmcl.2011.01.062
  • Primary Citation of Related Structures:  
    3ORN, 3OS3

  • PubMed Abstract: 

    The MAP kinase pathway is one of the most important pathways involved in cell proliferation and differentiation, and its components are promising targets for antitumor drugs. Design and synthesis of a novel MEK inhibitor, based on the 3D-structural information of the target enzyme, and then multidimensional optimization including metabolic stability, physicochemical properties and safety profiles were effectively performed and led to the identification of a clinical candidate for an orally available potent MEK inhibitor, CH4987655, possessing a unique 3-oxo-oxazinane ring structure at the 5-position of the benzamide core structure. CH4987655 exhibits slow dissociation from the MEK enzyme, remarkable in vivo antitumor efficacy both in mono- and combination therapy, desirable metabolic stability, and insignificant MEK inhibition in mouse brain, implying few CNS-related side effects in human. An excellent PK profile and clear target inhibition in PBMC were demonstrated in a healthy volunteer clinical study.

  • Organizational Affiliation

    Kamakura Research Laboratories, Chugai Pharmaceutical Co., Ltd, Kamakura, Kanagawa, Japan. isshikiysa@chugai-pharm.co.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1307Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q02750 (Homo sapiens)
Explore Q02750 
Go to UniProtKB:  Q02750
PHAROS:  Q02750
GTEx:  ENSG00000169032 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02750
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ATP

Download Ideal Coordinates CCD File 
C10 H16 N5 O13 P3
Query on 3OS

Download Ideal Coordinates CCD File 
C [auth A]2-[(4-ethynyl-2-fluorophenyl)amino]-3,4-difluoro-N-(2-hydroxyethoxy)-5-{[(2-hydroxyethoxy)imino]methyl}benzamide
C20 H18 F3 N3 O5
Query on MG

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
3OS PDBBind:  3OS3 IC50: 235 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.268 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.998α = 90
b = 72.998β = 90
c = 131.505γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-27
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations