5QYG

PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment F2X-Entry F08a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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: 10.1016/j.str.2020.04.019
  • Primary Citation of Related Structures:  
    5R3W, 5R3V, 5R3Y, 5R3X, 5R3Z, 5QY6, 5QY5, 5QY8, 5QY7, 5QY9, 5QY2, 5QY1, 5QY4, 5QY3, 5QYV, 5QZ7, 5QYU, 5QZ6, 5QYX, 5QZ9, 5QYW, 5QZ8, 5QYZ, 5QYY, 5QYN, 5QYM, 5QYP, 5QZ1, 5QYO, 5QZ0, 5QYR, 5QZ3, 5QYQ, 5QZ2, 5QYT, 5QZ5, 5QYS, 5QZ4, 5QYF, 5QYE, 5QYH, 5QYG, 5QYJ, 5QYI, 5QYL, 5QYK, 5QYB, 5QYA, 5QYD, 5QYC

  • 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 ...

    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

    Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany. Electronic address: msweiss@helmholtz-berlin.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8A258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP8DBF3DNA39RNA8SLT21USA2YHR165C
UniProt
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33334 
Go to UniProtKB:  P33334
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
A1 cistron-splicing factor AAR2B308Saccharomyces 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBJ (Subject of Investigation/LOI)
Query on RBJ

Download Ideal Coordinates CCD File 
F [auth B]4-[(methylamino)methyl]phenol
C8 H11 N O
AMKMYXVFAOJGGQ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PGR
Query on PGR

Download Ideal Coordinates CCD File 
D [auth A]R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.116α = 90
b = 82.033β = 107.7
c = 92.973γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release