6YNM

Crystal structure of YTHDC1 with compound DHU_DC1_096


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.231 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted P1QClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structure-based design of ligands of the m6A-RNA reader YTHDC1

Li, Y.Bedi, R.K.Nai, F.von Roten, V.Dolbois, A.Zalesak, F.Nachawati, R.Huang, D.Caflisch, A.

(2022) Eur J Med Chem Rep 5: 100057


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
PHAROS:  Q96MU7
GTEx:  ENSG00000083896 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96MU7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P1Q (Subject of Investigation/LOI)
Query on P1Q

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]
1-[(2~{R},5~{S})-2-(3-chlorophenyl)-5-methyl-morpholin-4-yl]-3-methoxy-propan-2-ol
C15 H22 Cl N O3
TXSZONYEDFRDCI-NGKXAEKTSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.4α = 90
b = 102.91β = 105.784
c = 42.11γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted P1QClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030B_189363

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description