3ORN

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1A307Homo sapiensMutation(s): 0 
Gene Names: MAP2K1, MEK1, PRKMK1
EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02750 (Homo sapiens)
Explore Q02750 
Go to UniProtKB:  Q02750
PHAROS:  Q02750
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02750
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3OR
Query on 3OR
Download Ideal Coordinates CCD File 
D [auth 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
ANP
Query on ANP
Download Ideal Coordinates CCD File 
B [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 Ligand Interaction
PGE
Query on PGE
Download Ideal Coordinates CCD File 
E [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3OR PDBBind:  3ORN Kd: 0.24 (nM) from 1 assay(s)
BindingDB:  3ORN Kd: min: 0.24, max: 8.7 (nM) from 2 assay(s)
IC50: 8.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.67α = 90
b = 136.67β = 90
c = 60.906γ = 120
Software Package:
Software NamePurpose
CNXrefinement
DENZOdata reduction
SCALAdata scaling
CNXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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