9MB3 | pdb_00009mb3

Crystal structure of YTHDC1 in complex with YL-5092


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Small-molecule inhibition of YTHDC1 as a strategy against acute myeloid leukemia in mouse models.

Zhang, H.Li, Y.Zhao, Y.Wang, F.Lin, G.Niu, T.Li, H.Li, Y.Liu, L.Liang, Y.Shen, Y.Yi, Y.Zhou, H.Lou, S.Ye, Y.He, Y.Yang, R.Yao, R.Tian, C.Zhou, P.Wu, M.Chen, M.Xu, H.You, J.Liao, Y.Yang, C.Zhao, A.Chen, C.Li, L.Pei, S.Yang, S.

(2026) Sci Transl Med 18: eadu3137-eadu3137

  • DOI: https://doi.org/10.1126/scitranslmed.adu3137
  • Primary Citation Related Structures: 
    9MB3, 9V84

  • PubMed Abstract: 

    Dysregulation of RNA N 6 -methyladenosine (m 6 A) readers has been linked to various diseases, but the therapeutic potential of small-molecule inhibitors targeting them is of interest. Here, we reported the identification and characterization of a potent and selective first-in-class inhibitor (YL-5092) of YTHDC1, a nuclear RNA m 6 A reader. We provided a high-resolution cocrystal structure of the YTHDC1-YL-5092 complex. In acute myeloid leukemia (AML) models, YL-5092 blocked the binding of YTHDC1 to its m 6 A substrates and reduced mRNA stability, resulting in apoptosis of AML cells and myeloid differentiation. In multiple xenograft models of AML representing disease heterogeneity, YL-5092 alone or in combination with standard AML therapy eliminated leukemia and extended survival. Moreover, YL-5092 functionally impaired leukemia stem cells yet spared normal hematopoietic counterparts. Collectively, our work demonstrates the efficacy of a selective YTHDC1 inhibitor and suggests that targeting of m 6 A readers is a potential strategy in the treatment of hematologic cancers.


  • Organizational Affiliation
    • Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.

Macromolecule Content 

  • Total Structure Weight: 39.14 kDa 
  • Atom Count: 3,040 
  • Modeled Residue Count: 330 
  • Deposited Residue Count: 330 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
YTH domain-containing protein 1
A, B
165Homo sapiensMutation(s): 0 
Gene Names: YTHDC1KIAA1966YT521
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ND0
(Subject of Investigation/LOI)

Query on ND0



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
N-[4-(1,3-thiazol-5-yl)phenyl]-4-[2-(trifluoromethyl)phenyl]carbonyl-1H-pyrrole-2-carboxamide
C22 H14 F3 N3 O2 S
HLKQNAGWYQKBSH-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.152α = 90
b = 74.405β = 90
c = 75.539γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-04-15
    Changes: Database references