3ZLW

Crystal structure of MEK1 in complex with fragment 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report



Literature

The Use of Virtual Screening and Differential Scanning Fluorimetry for the Rapid Identification of Fragments Active Against Mek1.

Amaning, K.Lowinski, M.Vallee, F.Steier, V.Marcireau, C.Ugolini, A.Delorme, C.Foucalt, F.Mccort, G.Derimay, N.Andouche, C.Vougier, S.Llopart, S.Halland, N.Rak, A.

(2013) Bioorg Med Chem Lett 23: 3620

  • DOI: 10.1016/j.bmcl.2013.04.003
  • Primary Citation of Related Structures:  
    3ZLW, 3ZLX, 3ZLY, 3ZLS, 3ZM4

  • PubMed Abstract: 
  • We report the analysis of an in-house fragment screening campaign for the oncology target MEK1. The application of virtual screening (VS) as a primary fragment screening approach, followed by biophysical validation using differential screening fluorimetry (DSF), with resultant binding mode determination by X-ray crystallography (X-ray), is presented as the most time and cost-effective combination of in silico and in vitro methods to identify fragments ...

    We report the analysis of an in-house fragment screening campaign for the oncology target MEK1. The application of virtual screening (VS) as a primary fragment screening approach, followed by biophysical validation using differential screening fluorimetry (DSF), with resultant binding mode determination by X-ray crystallography (X-ray), is presented as the most time and cost-effective combination of in silico and in vitro methods to identify fragments. We demonstrate the effectiveness of the VS-DSF workflow for the early identification of fragments to both 'jump-start' the drug discovery project and to complement biochemical screening data.


    Organizational Affiliation

    Sanofi, Structure Design and Informatics,13 Quai Guesde, B.P.14, F-94408 Vitry-Sur-Seine, France. kwame.amaning@sanofi.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 MAPK/ERK KINASE 1, MEK 1, MEK1A348Homo sapiensMutation(s): 3 
Gene Names: MAP2K1MEK1PRKMK1
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
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MT8
Query on MT8

Download CCD File 
A
(1R)-1-hydroxy-1-methyl-2,3,6,7-tetrahydro-1H,5H-pyrido[3,2,1-ij]quinolin-5-one
C13 H15 N O2
FHMNDLFMEHZYLO-CYBMUJFWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MT8IC50:  198000   nM  Binding MOAD
MT8IC50 :  198000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.059α = 90
b = 77.059β = 90
c = 221.8γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Database references
  • Version 1.2: 2018-05-02
    Changes: Data collection
  • Version 2.0: 2019-04-24
    Changes: Atomic model, Data collection, Source and taxonomy