3ORN

Mitogen-activated protein kinase kinase 1 (MEK1) in complex with CH4987655 and MgAMP-PNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.bmcl.2011.01.062
  • Primary Citation of Related Structures:  

  • 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 i ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dual specificity mitogen-activated protein kinase kinase 1
A
307Homo 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3OR
Query on 3OR

Download SDF File 
Download CCD File 
A
3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)-5-[(3-oxo-1,2-oxazinan-2-yl)methyl]benzamide
C20 H19 F3 I N3 O5
FIMYFEGKMOCQKT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ANP
Query on ANP

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

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

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3ORKd: 0.2 - 8.7 nM (90) BINDINGDB
3ORIC50: 8.8 nM (90) BINDINGDB
3ORKd: 0.24 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.234 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.670α = 90.00
b = 136.670β = 90.00
c = 60.906γ = 120.00
Software Package:
Software NamePurpose
CNXphasing
CNXrefinement
SCALAdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-23
    Type: Data collection, Refinement description, Source and taxonomy