2P55 | pdb_00002p55

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: 2.80 Å
  • R-Value Free: 
    0.301 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.226 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2P55

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

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: 5090-5102

  • DOI: https://doi.org/10.1021/jm0704548
  • Primary Citation Related Structures: 
    2P55

  • PubMed Abstract: 

    A new series of MEK1 inhibitors, the 4-anilino-5-carboxamido-2-pyridones, were designed and synthesized using a combination of medicinal chemistry, computational chemistry, and structural elucidation. The effect of variation in the carboxamide side chain, substitution on the pyridone nitrogen, and replacement of the 4'-iodide were all investigated. This study afforded several compounds which were either equipotent or more potent than the clinical candidate CI-1040 (1) in an isolated enzyme assay, as well as murine colon carcinoma (C26) cells, as measured by suppression of phosphorylated ERK substrate. Most notably, pyridone 27 was found to be more potent than 1 in vitro and produced a 100% response rate at a lower dose than 1, when tested for in vivo efficacy in animals bearing C26 tumors.


  • Organizational Affiliation
    • Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. j.spicer@auckland.ac.nz

Macromolecule Content 

  • Total Structure Weight: 37.74 kDa 
  • Atom Count: 2,356 
  • Modeled Residue Count: 289 
  • Deposited Residue Count: 333 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1333Homo sapiensMutation(s): 0 
Gene Names: MAP2K1MEK1PRKMK1
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
GTEx:  ENSG00000169032 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02750
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP



Download:Ideal Coordinates CCD File
D [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MRA

Query on MRA



Download:Ideal Coordinates CCD File
C [auth A]2-[(4-ETHYNYL-2-FLUOROPHENYL)AMINO]-3,4-DIFLUORO-N-(2-HYDROXYETHOXY)BENZAMIDE
C17 H13 F3 N2 O3
AMNKRBRQQAMACZ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.301 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.226 (DCC) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.634α = 90
b = 81.634β = 90
c = 129.086γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description