5BX0

An Automated Microscale Thermophoresis Screening Approach for Fragment-Based Lead Discovery


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An Automated Microscale Thermophoresis Screening Approach for Fragment-Based Lead Discovery.

Linke, P.Amaning, K.Maschberger, M.Vallee, F.Steier, V.Baaske, P.Duhr, S.Breitsprecher, D.Rak, A.

(2016) J Biomol Screen 21: 414-421

  • DOI: https://doi.org/10.1177/1087057115618347
  • Primary Citation of Related Structures:  
    5BX0

  • PubMed Abstract: 

    Fragment-based lead discovery has proved to be an effective alternative to high-throughput screenings in identifying chemical matter that can be developed into robust lead compounds. The search for optimal combinations of biophysical techniques that can correctly and efficiently identify and quantify binding can be challenging due to the physicochemical properties of fragments. In order to minimize the time and costs of screening, optimal combinations of biophysical techniques with maximal information content, sensitivity, and robustness are needed. Here we describe an approach utilizing automated microscale thermophoresis (MST) affinity screening to identify fragments active against MEK1 kinase. MST identified multiple hits that were confirmed by X-ray crystallography but not detected by orthogonal methods. Furthermore, MST also provided information about ligand-induced aggregation and protein denaturation. The technique delivered a large number of binders while reducing experimentation time and sample consumption, demonstrating the potential of MST to execute and maximize the efficacy of fragment screening campaigns.


  • Organizational Affiliation

    NanoTemper Technologies GmbH, Munich, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1348Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4W5
Query on 4W5

Download Ideal Coordinates CCD File 
B [auth A]ethyl 2H-indazole-5-carboxylate
C10 H10 N2 O2
SKABXDPLIJIWLR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.402α = 90
b = 75.402β = 90
c = 223.768γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
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: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description