5SU8

PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment P03F01 from the F2X-Universal Library


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 ?
  • R-Value Free: 0.255 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Large-Scale Crystallographic Fragment Screening Expedites Compound Optimization and Identifies Putative Protein-Protein Interaction Sites.

Barthel, T.Wollenhaupt, J.Lima, G.M.A.Wahl, M.C.Weiss, M.S.

(2022) J Med Chem 65: 14630-14641

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01165
  • Primary Citation of Related Structures:  
    5ST0, 5ST1, 5ST2, 5ST3, 5ST4, 5ST5, 5ST6, 5ST7, 5ST8, 5ST9, 5STA, 5STB, 5STC, 5STE, 5STF, 5STG, 5STH, 5STI, 5STJ, 5STK, 5STL, 5STM, 5STN, 5STO, 5STP, 5STQ, 5STR, 5STS, 5STT, 5STU, 5STV, 5STW, 5STX, 5STY, 5STZ, 5SU0, 5SU1, 5SU2, 5SU3, 5SU4, 5SU5, 5SU6, 5SU7, 5SU8, 5SU9, 5SUA, 5SUB, 5SUC, 5SUD, 5SUE

  • PubMed Abstract: 

    The identification of starting points for compound development is one of the key steps in early-stage drug discovery. Information-rich techniques such as crystallographic fragment screening can potentially increase the efficiency of this step by providing the structural information of the binding mode of the ligands in addition to the mere binding information. Here, we present the crystallographic screening of our 1000-plus-compound F2X-Universal Library against the complex of the yeast spliceosomal Prp8 RNaseH-like domain and the snRNP assembly factor Aar2. The observed 269 hits are distributed over 10 distinct binding sites on the surface of the protein-protein complex. Our work shows that hit clusters from large-scale crystallographic fragment screening campaigns identify known interaction sites with other proteins and suggest putative additional interaction sites. Furthermore, the inherent binding pose validation within the hit clusters may accelerate downstream compound optimization.


  • Organizational Affiliation

    Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Stra?e 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
V40
Query on V40

Download Ideal Coordinates CCD File 
C [auth A](2S)-1-{[(1R,2R)-2-(aminomethyl)cyclohexyl]methyl}pyrrolidin-2-ol
C12 H24 N2 O
ITLMVPHXKPDLDM-SRVKXCTJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 ?
  • R-Value Free: 0.255 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( ? )Angle ( ? )
a = 89.789¦Á = 90
b = 81.642¦Â = 108.79
c = 92.984¦Ă = 90
Software Package:
Software NamePurpose
xdsappdata processing
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection
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