3PP1

Crystal Structure of the Human Mitogen-activated protein kinase kinase 1 (MEK 1) in complex with ligand and MgATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of TAK-733, a potent and selective MEK allosteric site inhibitor for the treatment of cancer.

Dong, Q.Dougan, D.R.Gong, X.Halkowycz, P.Jin, B.Kanouni, T.O'Connell, S.M.Scorah, N.Shi, L.Wallace, M.B.Zhou, F.

(2011) Bioorg Med Chem Lett 21: 1315-1319

  • DOI: 10.1016/j.bmcl.2011.01.071
  • Primary Citation of Related Structures:  
    3PP1

  • PubMed Abstract: 
  • A novel 5-phenylamino-8-methylpyrido[2,3-d]pyrimidine-4,7(3H,8H)-dione series of MEK inhibitors has been developed using structure-based drug design. Lead optimization of this series led to the discovery of TAK-733. This was advanced to Phase I clinical studies for cancer treatment ...

    A novel 5-phenylamino-8-methylpyrido[2,3-d]pyrimidine-4,7(3H,8H)-dione series of MEK inhibitors has been developed using structure-based drug design. Lead optimization of this series led to the discovery of TAK-733. This was advanced to Phase I clinical studies for cancer treatment.


    Organizational Affiliation

    Takeda San Diego, San Diego, CA 92121, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1A328Homo sapiensMutation(s): 0 
Gene Names: MAP2K1Mapk/erk kinase 1MEK1PRKMK1
EC: 2.7.12.2
Find proteins for Q02750 (Homo sapiens)
Explore Q02750 
Go to UniProtKB:  Q02750
NIH Common Fund Data Resources
PHAROS  Q02750
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

Download CCD File 
A
3-[(2R)-2,3-dihydroxypropyl]-6-fluoro-5-[(2-fluoro-4-iodophenyl)amino]-8-methylpyrido[2,3-d]pyrimidine-4,7(3H,8H)-dione
C17 H15 F2 I N4 O4
RCLQNICOARASSR-SECBINFHSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IZGIC50:  6.900000095367432   nM  BindingDB
IZGIC50:  1.7999999523162842   nM  BindingDB
IZGIC50:  5   nM  BindingDB
IZGIC50:  3.200000047683716   nM  BindingDB
IZGIC50 :  3.200000047683716   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.086α = 90
b = 82.086β = 90
c = 129.254γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-11-23 
  • Released Date: 2011-02-23 
  • Deposition Author(s): Dougan, D.R.

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description