7P88

Crystal structure of YTHDC1 with compound YLI_DC1_002

• PDB DOI: https://doi.org/10.2210/pdb7P88/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-21 Released: 2021-10-20 
• Deposition Author(s): Bedi, R.K., Li, Y., Dolbois, A., Caflisch, A.
• Funding Organization(s): Swiss National Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

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

• DOI: https://doi.org/10.1016/j.ejmcr.2022.100057

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.78 kDa 
• Atom Count: 3,081 
• Modelled Residue Count: 328 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing protein 1	A, B	183	Homo sapiens	Mutation(s): 0  Gene Names: YTHDC1, KIAA1966, YT521
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MU7 (Homo sapiens) Explore Q96MU7  Go to UniProtKB:  Q96MU7
PHAROS:  Q96MU7 GTEx:  ENSG00000083896

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OYN (Subject of Investigation/LOI)	C [auth A], E [auth B]	2-chloranyl-~{N}-methyl-9~{H}-purin-6-amine C6 H6 Cl N5 RIAVUEFUPHOGJY-UHFFFAOYSA-N
SO4	D [auth A], F [auth B], G [auth B], H [auth B], 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:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.81	α = 90
b = 103.6	β = 105.66
c = 42.03	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-20 
Deposition Author(s): Bedi, R.K., Li, Y., Dolbois, A., Caflisch, A.

---

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_189363

Revision History  

• Version 1.0: 2021-10-20
  Type: Initial release
  
• Version 2.0: 2022-06-15
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2024-01-31
  Changes: Data collection, Refinement description