5R0F

PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry D06, DMSO-free


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening.

Wollenhaupt, J.Metz, A.Barthel, T.Lima, G.M.A.Heine, A.Mueller, U.Klebe, G.Weiss, M.S.

(2020) Structure 28: 694-706.e5

  • DOI: https://doi.org/10.1016/j.str.2020.04.019
  • Primary Citation of Related Structures:  
    5QY1, 5QY2, 5QY3, 5QY4, 5QY5, 5QY6, 5QY7, 5QY8, 5QY9, 5QYA, 5QYB, 5QYC, 5QYD, 5QYE, 5QYF, 5QYG, 5QYH, 5QYI, 5QYJ, 5QYK, 5QYL, 5QYM, 5QYN, 5QYO, 5QYP, 5QYQ, 5QYR, 5QYS, 5QYT, 5QYU, 5QYV, 5QYW, 5QYX, 5QYY, 5QYZ, 5QZ0, 5QZ1, 5QZ2, 5QZ3, 5QZ4, 5QZ5, 5QZ6, 5QZ7, 5QZ8, 5QZ9, 5QZA, 5QZB, 5QZC, 5QZD, 5QZE

  • PubMed Abstract: 

    Crystallographic fragment screening (CFS) provides excellent starting points for projects concerned with drug discovery or biochemical tool compound development. One of the fundamental prerequisites for effective CFS is the availability of a versatile fragment library. Here, we report on the assembly of the 1,103-compound F2X-Universal Library and its 96-compound sub-selection, the F2X-Entry Screen. Both represent the available fragment chemistry and are highly diverse in terms of their 3D-pharmacophore variations. Validation of the F2X-Entry Screen in CFS campaigns using endothiapepsin and the Aar2/RNaseH complex yielded hit rates of 30% and 21%, respectively, and revealed versatile binding sites. Dry presentation of the libraries allows CFS campaigns to be carried out with or without the co-solvent DMSO present. Most of the hits in our validation campaigns could be reproduced also in the absence of DMSO. Consequently, CFS can be carried out more efficiently and for a wider range of conditions and targets.


  • Organizational Affiliation

    Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany; Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8DBF3DNA39RNA8SLT21USA2YHR165C
UniProt
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33334 
Go to UniProtKB:  P33334
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33334
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
A1 cistron-splicing factor AAR2308Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: AAR2YBL074CYBL06.06YBL0611
UniProt
Find proteins for P32357 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32357 
Go to UniProtKB:  P32357
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32357
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R9G (Subject of Investigation/LOI)
Query on R9G

Download Ideal Coordinates CCD File 
C [auth A](3-methoxyphenyl)(pyrrolidin-1-yl)methanone
C12 H15 N O2
WMEQIJXKEGOFTK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.263 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.59α = 90
b = 82.24β = 108.25
c = 91.639γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2021-03-10
    Changes: Data collection
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references