4TY8

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: 0.268 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 1.3 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: 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 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] Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PolyproteinA, C, D566Hepacivirus CMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for D0PY27 (Hepacivirus C)
Explore D0PY27 
Go to UniProtKB:  D0PY27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0PY27
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PolyproteinB566Hepacivirus CMutation(s): 1 
EC: 2.7.7.48
UniProt
Find proteins for D0PY27 (Hepacivirus C)
Explore D0PY27 
Go to UniProtKB:  D0PY27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0PY27
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3AV
Query on 3AV
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		6-methyl-2H-chromen-2-one
C10 H8 O2
FXFYOPQLGGEACP-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.937α = 90
b = 102.07β = 90
c = 251.925γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data extraction
HKL-3000data processing
PHASERphasing
REFMACrefinement
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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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