7Z8X

Crystal structure of YTHDF2 with compound YLI_DC1_017

• PDB DOI: https://doi.org/10.2210/pdb7Z8X/pdb

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


• Deposited: 2022-03-18 Released: 2022-04-06 
• Deposition Author(s): Nachawati, R., Nai, F., Li, Y., Caflisch, A.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.238 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Fragment Ligands of the m 6 A-RNA Reader YTHDF2.

Nai, F., Nachawati, R., Zalesak, F., Wang, X., Li, Y., Caflisch, A.

(2022) ACS Med Chem Lett 13: 1500-1509

• PubMed: 36110386 
• DOI: https://doi.org/10.1021/acsmedchemlett.2c00303
• Primary Citation of Related Structures:  
  7R5F, 7R5L, 7R5W, 7YWB, 7YX6, 7YXE, 7Z26, 7Z4U, 7Z54, 7Z5M, 7Z7B, 7Z7F, 7Z8P, 7Z8W, 7Z8X, 7Z92, 7Z93, 7ZG4


• PubMed Abstract: 
  

  We report 17 small-molecule ligands that compete with N6 -methyladenosine (m ⁶ A) for binding to the m ⁶ A-reader domain of YTHDF2 (YT521-B homology domain family 2). We determined their binding mode at high resolution by X-ray crystallography and quantified their affinity by a fluorescence-based binding assay. 6-Cyclopropyluracil and a pyrazolopyrimidine derivative have favorable ligand efficiencies of 0.47 and 0.38 kcal mol ^-1 per non-hydrogen atom, respectively. They represent useful starting points for hit optimization.

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Organizational Affiliation: 

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

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: 39.36 kDa 
• Atom Count: 2,594 
• Modelled Residue Count: 297 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing family protein 2	A, B	167	Homo sapiens	Mutation(s): 0  Gene Names: YTHDF2, HGRG8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5A9 (Homo sapiens) Explore Q9Y5A9  Go to UniProtKB:  Q9Y5A9
PHAROS:  Q9Y5A9 GTEx:  ENSG00000198492

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IGX (Subject of Investigation/LOI)	C [auth A]	6-methoxy-1H-pyrimidine-2,4-dione C5 H6 N2 O3 SWNDNOHEVRPIDI-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.238 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.82	α = 90
b = 79.82	β = 90
c = 114.88	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Nachawati, R., Nai, F., Li, Y., Caflisch, A.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B-189363

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2022-05-04
  Changes: Database references, Structure summary
• Version 1.2: 2022-09-28
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description