3DV3

MEK1 with PF-04622664 Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Beyond the MEK-pocket: can current MEK kinase inhibitors be utilized to synthesize novel type III NCKIs? Does the MEK-pocket exist in kinases other than MEK?

Tecle, H.Shao, J.Li, Y.Kothe, M.Kazmirski, S.Penzotti, J.Ding, Y.H.Ohren, J.Moshinsky, D.Coli, R.Jhawar, N.Bora, E.Jacques-O'Hagan, S.Wu, J.

(2009) Bioorg.Med.Chem.Lett. 19: 226-229

  • DOI: 10.1016/j.bmcl.2008.10.108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An approach and preliminary results for utilizing legacy MEK inhibitors as templates for a reiterative structural based design and synthesis of novel, type III NCKIs (non-classical kinase inhibitors) is described. Evidence is provided that the MEK-po ...

    An approach and preliminary results for utilizing legacy MEK inhibitors as templates for a reiterative structural based design and synthesis of novel, type III NCKIs (non-classical kinase inhibitors) is described. Evidence is provided that the MEK-pocket or pockets closely related to it may exist in kinases other than MEK.


    Organizational Affiliation

    Pfizer Global Research and Development, Research Technology Center, Cambridge, MA 02139, USA. haile.tecle@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dual specificity mitogen-activated protein kinase kinase 1
A
322Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MEK
Query on MEK

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Download CCD File 
A
3,4-difluoro-2-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)-5-[(2-hydroxyethoxy)methyl]benzamide
C18 H18 F3 I N2 O5
PVBOBALIHWFPSS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MEKIC50: 21 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 81.596α = 90.00
b = 81.596β = 90.00
c = 129.966γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description