3EQB

X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in a complex with ligand and MgATP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

2-Alkylamino- and alkoxy-substituted 2-amino-1,3,4-oxadiazoles-O-Alkyl benzohydroxamate esters replacements retain the desired inhibition and selectivity against MEK (MAP ERK kinase).

Warmus, J.S., Flamme, C., Zhang, L.Y., Barrett, S., Bridges, A., Chen, H., Gowan, R., Kaufman, M., Sebolt-Leopold, J., Leopold, W., Merriman, R., Ohren, J., Pavlovsky, A., Przybranowski, S., Tecle, H., Valik, H., Whitehead, C., Zhang, E.

(2008) Bioorg Med Chem Lett 18: 6171-6174

  • DOI: 10.1016/j.bmcl.2008.10.015
  • Primary Citation of Related Structures:  
    3EQB

  • PubMed Abstract: 

    • This paper reports a second generation MEK inhibitor. The previously reported potent and efficacious MEK inhibitor, PD-184352 (CI-1040), contains an integral hydroxamate moiety. This compound suffered from less than ideal solubility and metabolic stability ...

    This paper reports a second generation MEK inhibitor. The previously reported potent and efficacious MEK inhibitor, PD-184352 (CI-1040), contains an integral hydroxamate moiety. This compound suffered from less than ideal solubility and metabolic stability. An oxadiazole moiety behaves as a bioisostere for the hydroxamate group, leading to a more metabolically stable and efficacious MEK inhibitor.

    Related Citations: 
    • 4-anilino-5-carboxamido-2-pyridone derivatives as noncompetitive inhibitors of mitogen-activated protein kinase kinase.
      Spicer, J.A., Rewcastle, G.W., Kaufman, M.D., Black, S.L., Plummer, M.S., Denny, W.A., Quin, J., Shahripour, A.B., Barrett, S.D., Whitehead, C.E., Milbank, J.B., Ohren, J.F., Gowan, R.C., Omer, C., Camp, H.S., Esmaeil, N., Moore, K., Sebolt-Leopold, J.S., Pryzbranowski, S., Merriman, R.L., Ortwine, D.F., Warmus, J.S., Flamme, C.M., Pavlovsky, A.G., Tecle, H.
      (2007) J Med Chem 50: 5090
    • Structures of human MAP kinase kinase 1 (MEK1) and MEK2 describe novel noncompetitive kinase inhibition.
      Ohren, J.F., Chen, H., Pavlovsky, A., Whitehead, C., Zhang, E., Kuffa, P., Yan, C., McConnell, P., Spessard, C., Banotai, C., Mueller, W.T., Delaney, A., Omer, C., Sebolt-Leopold, J., Dudley, D.T., Leung, I.K., Flamme, C., Warmus, J., Kaufman, M., Barrett, S., Tecle, H., Hasemann, C.A.
      (2004) Nat Struct Mol Biol 11: 1192
    Organizational Affiliation: 

    Department of Chemistry, Pfizer Global Research and Development, Ann Arbor, MI 48105, USA. Joseph.Warmus@Pfizer.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1A333Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
LUG
Query on LUG
Download Ideal Coordinates CCD File 
D [auth A]N-(5-{3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]phenyl}-1,3,4-oxadiazol-2-yl)ethane-1,2-diamine
C16 H13 F3 I N5 O
FPDWDLAITHFTTP-UHFFFAOYSA-N		 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
LUG PDBBind:  3EQB IC50: 1.50e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.128α = 90
b = 82.128β = 90
c = 129.099γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance