6T0A

Crystal structure of YTHDC1 with fragment 25 (PSI_DC1_005)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.182 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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
YTHDC1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M58 (Subject of Investigation/LOI)
Query on M58

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
(~{R})-azanyl(pyridin-3-yl)methanethiol
C6 H8 N2 S
FNWRZJSHJIXOOI-ZCFIWIBFSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.623α = 90
b = 102.925β = 105.727
c = 42.049γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

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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: Advisory, Data collection, Database references, Refinement description