Crystal structure of YTHDC1 with fragment 30 (DHU_DC1_220)

Experimental Data Snapshot

  • Resolution: 1.46 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
183Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MU7 (Homo sapiens)
Explore Q96MU7 
Go to UniProtKB:  Q96MU7
GTEx:  ENSG00000083896 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96MU7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.46 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.947α = 90
b = 103.461β = 105.17
c = 42.467γ = 90
Software Package:
Software NamePurpose
XDSdata reduction

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 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description