3MBL

Crystal Structure of the human mitogen-activated protein kinase kinase 1 (MEK 1) in complex with ligand and MgADP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Structure-based design and synthesis of pyrrole derivatives as MEK inhibitors.

Wallace, M.B., Adams, M.E., Kanouni, T., Mol, C.D., Dougan, D.R., Feher, V.A., O'Connell, S.M., Shi, L., Halkowycz, P., Dong, Q.

(2010) Bioorg Med Chem Lett 20: 4156-4158

  • DOI: https://doi.org/10.1016/j.bmcl.2010.05.058
  • Primary Citation of Related Structures:  
    3MBL

  • PubMed Abstract: 

    A novel series of pyrrole inhibitors of MEK kinase has been developed using structure-based drug design. Optimization of the series led to the identification of potent inhibitors with good pharmaceutical properties.

    • Organizational Affiliation: 

    Takeda San Diego, 10410 Science Center Drive, San Diego, CA 92121, United States. michael.wallace@takedasd.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1328Homo sapiensMutation(s): 0 
Gene Names: MAP2K1, MEK 1, 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
GTEx:  ENSG00000169032 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02750
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LSG
Query on LSG
Download Ideal Coordinates CCD File 
D [auth A]5-acetyl-2-[(2-fluoro-4-iodophenyl)amino]-N-(2-hydroxyethoxy)-1-methyl-1H-pyrrole-3-carboxamide
C16 H17 F I N3 O4
WRHOGNMBUWCIAC-UHFFFAOYSA-N
ADP
Query on ADP
Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
LSG PDBBind:  3MBL IC50: 18 (nM) from 1 assay(s)
BindingDB:  3MBL IC50: 18 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.982α = 90
b = 81.982β = 90
c = 129.928γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

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: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations