3ZLS

Crystal structure of MEK1 in complex with fragment 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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:  
    3ZLS, 3ZLW, 3ZLX, 3ZLY, 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 1A348Homo sapiensMutation(s): 3 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
92P (Subject of Investigation/LOI)
Query on 92P

Download Ideal Coordinates CCD File 
B [auth A]1H-PYRROLO[2,3-B]PYRIDINE-3-CARBOXYLIC ACID
C9 H8 N2 O2
XYRUNIAHPKBUJT-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
92P PDBBind:  3ZLS IC50: 3.94e+4 (nM) from 1 assay(s)
Binding MOAD:  3ZLS IC50: 3.94e+4 (nM) from 1 assay(s)
BindingDB:  3ZLS IC50: 3.94e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.683α = 90
b = 76.683β = 90
c = 221.983γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Database references