9VRA | pdb_00009vra

Small molecule 2-60 targeting YTHDC1

• PDB DOI: https://doi.org/10.2210/pdb9VRA/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-07-06 Released: 2026-11-11 
• Deposition Author(s): Fu, S., Wang, M., Chen, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.259 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: experimental

Literature

AS-TLC-Based High-Throughput Screening Integrated with CuAAC Optimization Strategy Facilitates the Rapid Discovery of YTHDC1 Inhibitor.

Wang, M., Fu, S., Xu, Y., Gao, J., Ren, J., Yang, X., Xu, H., Sun, G., Li, Y., Wang, Y., Jin, L., Chen, P., Xu, Y., Li, J., Lin, H., Hu, C., Chen, K., Xiong, H., Luo, C., Chen, S.

(2026) Adv Sci (Weinh) : e77386-e77386

• PubMed: 42658481 
• DOI: https://doi.org/10.1002/advs.77386
• Primary Citation Related Structures: 
  9VRA, 9VS9, 9VSB


• PubMed Abstract: 
  

  The classical sequential workflow-individual compound screening, followed by stepwise design-synthesis-purification of derivatives-makes lead compound discovery time-consuming and cost-prohibitive. Herein, we developed Affinity Selection Thin-Layer Chromatography (AS-TLC) as a method for high-throughput screening (HTS), enabling efficient and cost-effective screening of compound mixtures. Furthermore, we integrated activity assays with AS-TLC to minimize target protein consumption and lower the false positive rate, through which we identified a YTH domain-containing protein 1 (YTHDC1) inhibitor, fragment YD, with a half-maximal inhibitory concentration (IC ₅₀ ) of 20.01 ± 3.30 µm. Building on this hit, we applied copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry for rapid structural modification and compound library construction, ultimately obtaining LC-YD03 with significantly enhanced inhibitory activity (IC ₅₀  = 41.98 ± 6.24 nm). The interaction mode between LC-YD03 and YTHDC1 was further clarified via X-ray crystallographic analysis. This study demonstrates that the AS-TLC-activity assay platform enables efficient hit screening from compound mixtures; subsequent click chemistry-based combinatorial library technology accelerates lead compound optimization. Collectively, this workflow significantly reduces the time and cost associated with lead compound discovery.

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Organizational Affiliation: 
• School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
Precision Medicine Research Institute of Guizhou, and Guizhou Provincial Key Laboratory of Digestive System Diseases, The Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guiyang, China.
Innovation Center for AI and Drug Discovery, School of Pharmacy, East China Normal University, Shanghai, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, China.
Tianfu Jincheng Laboratory, Chengdu, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 42.93 kDa 
• Atom Count: 2,681 
• Modeled Residue Count: 327 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing protein 1	A, B	187	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
A1ES8 (Subject of Investigation/LOI)	C [auth A], D [auth B]	2-chloranyl-~{N}-methyl-9-prop-2-ynyl-purin-6-amine C9 H8 Cl N5 OMEZSUZYARERFA-UHFFFAOYSA-N
SO4	E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.259 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.166	α = 90
b = 103.443	β = 102.29
c = 41.522	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-11 
Deposition Author(s): Fu, S., Wang, M., Chen, S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-11-11
  Type: Initial release