4TXS

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: 0.294 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


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, B, 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3AQ
Query on 3AQ

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
(4-hydroxyphenyl)acetonitrile
C8 H7 N O
AYKYOOPFBCOXSL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.177α = 90
b = 102.077β = 90
c = 251.875γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data extraction
HKL-3000data processing
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
REFMACrefinement
REFMACrefinement

Structure Validation

View Full Validation Report




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