8IT9

Co-crystal structure of FTO bound to 22

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

  • Deposited: 2023-03-22 Released: 2024-02-14 
  • Deposition Author(s): Yang, C.-G., Gan, J.H.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), National Key Research and Development Program of China

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Rational Design of RNA Demethylase FTO Inhibitors with Enhanced Antileukemia Drug-Like Properties.

Xiao, P.Duan, Z.Liu, Z.Chen, L.Zhang, D.Liu, L.Zhou, C.Gan, J.Dong, Z.Yang, C.G.

(2023) J Med Chem 66: 9731-9752

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00543
  • Primary Citation of Related Structures:  
    8IT9

  • PubMed Abstract: 

    The fat mass and obesity-associated protein (FTO) is an RNA N 6 -methyladenosine (m 6 A) demethylase highly expressed in diverse cancers including acute myeloid leukemia (AML). To improve antileukemia drug-like properties, we have designed 44 /ZLD115, a flexible alkaline side-chain-substituted benzoic acid FTO inhibitor derived from FB23. A combination of structure-activity relationship analysis and lipophilic efficiency-guided optimization demonstrates that 44 /ZLD115 exhibits better drug-likeness than the previously reported FTO inhibitors, FB23 and 13a /Dac85. Then, 44 /ZLD115 shows significant antiproliferative activity in leukemic NB4 and MOLM13 cell lines. Moreover, 44 /ZLD115 treatment noticeably increases m 6 A abundance on the AML cell RNA, upregulates RARA gene expression, and downregulates MYC gene expression in MOLM13 cells, which are consistent with FTO gene knockdown. Lastly, 44 /ZLD115 exhibits antileukemic activity in xenograft mice without substantial side effects. This FTO inhibitor demonstrates promising properties that can be further developed for antileukemia applications.


  • Organizational Affiliation

    School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-ketoglutarate-dependent dioxygenase FTO491Homo 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
ZL6 (Subject of Investigation/LOI)
Query on ZL6

Download Ideal Coordinates CCD File 
B [auth A]2-[(2,6-diethyl-4-pyridin-4-yl-phenyl)amino]-6-(1,4-oxazepan-4-ylmethyl)benzoic acid
C28 H33 N3 O3
DYKGFUNWMFFSJF-UHFFFAOYSA-N
AKG
Query on AKG

Download Ideal Coordinates CCD File 
C [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.189α = 90
b = 142.189β = 90
c = 84.358γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21725801
National Key Research and Development Program of ChinaChina2022YFC2705005

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release