9KNH | pdb_00009knh

Structural complex of FTO bound with Dac590

• PDB DOI: https://doi.org/10.2210/pdb9KNH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-18 Released: 2025-09-03 
• Deposition Author(s): Yang, C.G., Yang, T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Development of Orally Bioavailable FTO Inhibitors with Potent Antileukemia Efficacy.

Yang, T., Dong, Z., Du, R., Wang, Y., Liu, L., Xue, Y., Zhang, X., Liao, Y., Gan, J., Yu, X., Huang, Y., Yang, C.G.

(2025) J Med Chem 68: 13714-13727

• PubMed: 40579742 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c00566
• Primary Citation of Related Structures:  
  9KNH


• PubMed Abstract: 
  

  N ⁶ -Methyladenosine (m ⁶ A), the most prevalent mRNA modification, undergoes dynamic regulation mediated by the demethylase fat mass and obesity-associated protein (FTO), which is aberrantly overexpressed in acute myeloid leukemia (AML) and drives leukemogenesis. Based on the structure-guided optimization of our previously reported FTO inhibitor Dac85 and fluorescein, we developed Dac590 , a tricyclic benzoic acid derivative with potent FTO inhibitory activity and improved pharmacokinetic properties. Dac590 exerts a robust antiproliferative effect on AML cells by suppressing oncogenic FTO signaling. Oral administration of Dac590 significantly inhibited xenograft tumor growth and prolonged survival in AML mouse models with no observed toxicity. Notably, Dac590 synergized with decitabine to enhance DNA hypomethylation and further improve the survival rates. Our study identifies Dac590 as a potent orally bioavailable FTO inhibitor and demonstrates a combinatorial strategy through dual epigenetic modulations for enhanced AML therapy.

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Organizational Affiliation: 
• School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
University of the Chinese Academy of Sciences, Beijing 100049, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264117, China.
Rname Pharmaceutical Technology (Shanghai) Co., LTD., Shanghai 430048, China.
School of Life Sciences, Fudan University, Shanghai 200433, China.
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 55.53 kDa 
• Atom Count: 3,192 
• Modeled Residue Count: 425 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ketoglutarate-dependent dioxygenase FTO	A	478	Homo sapiens	Mutation(s): 0  Gene Names: FTO, KIAA1752 EC: 1.14.11 (PDB Primary Data), 1.14.11.53 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0B1 (Homo sapiens) Explore Q9C0B1  Go to UniProtKB:  Q9C0B1
PHAROS:  Q9C0B1 GTEx:  ENSG00000140718

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EF4	B [auth A]	2-[[2-chloranyl-4-(3,5-dimethyl-1,2-oxazol-4-yl)-6-fluoranyl-phenyl]amino]-5-methoxy-benzoic acid C19 H16 Cl F N2 O4 LPUCIEIAOLPFAI-UHFFFAOYSA-N
OGA	C [auth A]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
FE	D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.316	α = 90
b = 140.316	β = 90
c = 83.819	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Yang, C.G., Yang, T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21725801

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release