9KNI | pdb_00009kni

Structural complex of FTO bound with 12j


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9KNI

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Development of 3-arylaminothiophenic-2-carboxylic acid derivatives as new FTO inhibitors showing potent antileukemia activities.

Zhang, D.Liu, L.Li, M.Hu, X.Zhang, X.Xia, W.Wang, Z.Song, X.Huang, Y.Dong, Z.Yang, C.G.

(2025) Eur J Med Chem 289: 117444-117444

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117444
  • Primary Citation Related Structures: 
    9KNI

  • PubMed Abstract: 

    Fat mass and obesity-associated protein (FTO) is the first discovered RNA N 6 -methyladenosine (m 6 A) demethylase. The highly expressed FTO protein is required to trigger oncogenic pathways in acute myeloid leukemia (AML), which makes FTO a promising antileukemia drug target. In this study, we identify 3-arylaminothiophenic-2-carboxylic acid derivatives as new FTO inhibitors with good antileukemia activity. We replaced the phenyl A-ring in FB23, the first-generation of FTO inhibitor, with five-membered heterocycles and synthesized a new class of FTO inhibitors. Compound 12o/F97 shows strong enzymatic inhibitory activity and potent antiproliferative activity. 12o/F97 selectively inhibits m 6 A demethylation by FTO rather than ALKBH5, and has minimal effect on m 1 A demethylation by ALKBH3. Additionally, 12o/F97 increases the protein levels of RARA and ASB2, while decreasing that of MYC in AML cell lines. Lastly, 12o/F97 exhibits antileukemia activity in a xenograft mice model without significant side-effects. The identification of 3-arylaminothiophenic-2-carboxylic acid derivatives as new FTO inhibitors not only expands the chemical space but also holds potential for antileukemia drug development.


  • Organizational Affiliation
    • School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China.

Macromolecule Content 

  • Total Structure Weight: 55.46 kDa 
  • Atom Count: 3,510 
  • Modeled Residue Count: 434 
  • Deposited Residue Count: 478 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-ketoglutarate-dependent dioxygenase FTO478Homo sapiensMutation(s): 0 
Gene Names: FTOKIAA1752
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C0B1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EF5
(Subject of Investigation/LOI)

Query on A1EF5



Download:Ideal Coordinates CCD File
C [auth A]3-[[2,6-bis(chloranyl)-4-(3,5-dimethyl-1H-pyrazol-4-yl)phenyl]amino]thiophene-2-carboxylic acid
C16 H13 Cl2 N3 O2 S
LPPYVZNSYHOKKW-UHFFFAOYSA-N
AKG

Query on AKG



Download:Ideal Coordinates CCD File
B [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.41α = 90
b = 141.41β = 90
c = 83.85γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
HKL-3000data reduction
PHENIXphasing

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)China22077133

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release