4TY9

An Ligand-observed Mass Spectrometry-based Approach Integrated into the Fragment Based Lead Discovery Pipeline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3B0Click on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

A ligand-observed mass spectrometry approach integrated into the fragment based lead discovery pipeline

Chen, X.Qin, S.Chen, S.Li, J.Li, L.Wang, Z.Wang, Q.Lin, J.Yang, C.Shui, W.

(2015) Sci Rep 5: 8361-8361

  • DOI: https://doi.org/10.1038/srep08361
  • Primary Citation of Related Structures:  
    4TXS, 4TY8, 4TY9, 4TYA, 4TYB

  • PubMed Abstract: 

    In fragment-based lead discovery (FBLD), a cascade combining multiple orthogonal technologies is required for reliable detection and characterization of fragment binding to the target. Given the limitations of the mainstream screening techniques, we presented a ligand-observed mass spectrometry approach to expand the toolkits and increase the flexibility of building a FBLD pipeline especially for tough targets. In this study, this approach was integrated into a FBLD program targeting the HCV RNA polymerase NS5B. Our ligand-observed mass spectrometry analysis resulted in the discovery of 10 hits from a 384-member fragment library through two independent screens of complex cocktails and a follow-up validation assay. Moreover, this MS-based approach enabled quantitative measurement of weak binding affinities of fragments which was in general consistent with SPR analysis. Five out of the ten hits were then successfully translated to X-ray structures of fragment-bound complexes to lay a foundation for structure-based inhibitor design. With distinctive strengths in terms of high capacity and speed, minimal method development, easy sample preparation, low material consumption and quantitative capability, this MS-based assay is anticipated to be a valuable addition to the repertoire of current fragment screening techniques.


  • Organizational Affiliation

    1] College of Life Sciences, Nankai University, Tianjin 300071, China [2] High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyprotein
A, B, C, D
566Hepacivirus hominisMutation(s): 3 
EC: 2.7.7.48
UniProt
Find proteins for D0PY27 (Hepacivirus hominis)
Explore D0PY27 
Go to UniProtKB:  D0PY27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0PY27
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3B0
Query on 3B0

Download Ideal Coordinates CCD File 
E [auth A]5-(trifluoromethyl)pyridin-2-amine
C6 H5 F3 N2
RSGVKIIEIXOMPY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.774α = 90
b = 101.643β = 90
c = 251.582γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data collection
HKL-3000data extraction
HKL-3000data processing
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3B0Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Derived calculations
  • Version 1.2: 2015-09-02
    Changes: Data collection
  • Version 1.3: 2017-09-27
    Changes: Data collection, Derived calculations
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references, Source and taxonomy