6SZ7

Crystal structure of YTHDC1 with fragment 5 (DHU_DC1_066)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Selectively Disrupting m6A-Dependent Protein-RNA Interactions with Fragments.

Bedi, R.K.Huang, D.Wiedmer, L.Li, Y.Dolbois, A.Wojdyla, J.A.Sharpe, M.E.Caflisch, A.Sledz, P.

(2020) ACS Chem Biol 15: 618-625

  • DOI: https://doi.org/10.1021/acschembio.9b00894
  • Primary Citation of Related Structures:  
    6SYZ, 6SZ1, 6SZ2, 6SZ3, 6SZ7, 6SZ8, 6SZL, 6SZN, 6SZR, 6SZT, 6SZX, 6SZY, 6T01, 6T02, 6T03, 6T04, 6T05, 6T06, 6T07, 6T08, 6T09, 6T0A, 6T0C, 6T0D, 6T0O, 6T0X, 6T0Z, 6T10, 6T11, 6T12

  • PubMed Abstract: 

    We report a crystallographic analysis of small-molecule ligands of the human YTHDC1 domain that recognizes N6-methylated adenine (m 6 A) in RNA. The 30 binders are fragments (molecular weight < 300 g mol -1 ) that represent 10 different chemotypes identified by virtual screening. Despite the structural disorder of the binding site loop (residues 429-439), most of the 30 fragments emulate the two main interactions of the -NHCH 3 group of m 6 A. These interactions are the hydrogen bond to the backbone carbonyl of Ser378 and the van der Waals contacts with the tryptophan cage. Different chemical groups are involved in the conserved binding motifs. Some of the fragments show favorable ligand efficiency for YTHDC1 and selectivity against other m 6 A reader domains. The structural information is useful for the design of modulators of m 6 A recognition by YTHDC1.


  • Organizational Affiliation

    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YTH domain-containing protein 1
A, B
183Homo sapiensMutation(s): 0 
Gene Names: YTHDC1KIAA1966YT521
UniProt
Find proteins for A0A2K6KCS5 (Rhinopithecus bieti)
Explore A0A2K6KCS5 
Go to UniProtKB:  A0A2K6KCS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K6KCS5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.822α = 90
b = 103.574β = 105.085
c = 42.523γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
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: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 2.0: 2020-09-09
    Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description