7CKK | pdb_00007ckk

Structural complex of FTO bound with Dac51


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.264 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.223 (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 1.2 of the entry. See complete history

Literature

Tumors exploit FTO-mediated regulation of glycolytic metabolism to evade immune surveillance.

Liu, Y.Liang, G.Xu, H.Dong, W.Dong, Z.Qiu, Z.Zhang, Z.Li, F.Huang, Y.Li, Y.Wu, J.Yin, S.Zhang, Y.Guo, P.Liu, J.Xi, J.J.Jiang, P.Han, D.Yang, C.G.Xu, M.M.

(2021) Cell Metab 33: 1221-1233.e11

  • DOI: https://doi.org/10.1016/j.cmet.2021.04.001
  • Primary Citation Related Structures: 
    7CKK

  • PubMed Abstract: 

    The ever-increasing understanding of the complexity of factors and regulatory layers that contribute to immune evasion facilitates the development of immunotherapies. However, the diversity of malignant tumors limits many known mechanisms in specific genetic and epigenetic contexts, manifesting the need to discover general driver genes. Here, we have identified the m 6 A demethylase FTO as an essential epitranscriptomic regulator utilized by tumors to escape immune surveillance through regulation of glycolytic metabolism. We show that FTO-mediated m 6 A demethylation in tumor cells elevates the transcription factors c-Jun, JunB, and C/EBPβ, which allows the rewiring of glycolytic metabolism. Fto knockdown impairs the glycolytic activity of tumor cells, which restores the function of CD8 + T cells, thereby inhibiting tumor growth. Furthermore, we developed a small-molecule compound, Dac51, that can inhibit the activity of FTO, block FTO-mediated immune evasion, and synergize with checkpoint blockade for better tumor control, suggesting reprogramming RNA epitranscriptome as a potential strategy for immunotherapy.


  • Organizational Affiliation
    • Department of Basic Medical Sciences, School of Medicine, Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, THU-PKU Center for Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecule Content 

  • Total Structure Weight: 54.92 kDa 
  • Atom Count: 3,467 
  • Modeled Residue Count: 424 
  • Deposited Residue Count: 473 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-ketoglutarate-dependent dioxygenase FTO473Homo sapiensMutation(s): 1 
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B6C
(Subject of Investigation/LOI)

Query on B6C



Download:Ideal Coordinates CCD File
C [auth A]2-{[2,6-dichloro-4-(3,5-dimethyl-1H-pyrazol-4-yl)phenyl]amino}-N-hydroxybenzamide
C18 H16 Cl2 N4 O2
UMQKDDMRCQAIGA-UHFFFAOYSA-N
OGA

Query on OGA



Download:Ideal Coordinates CCD File
B [auth A]N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
OGA BindingDB:  7CKK IC50: min: 3.65e+4, max: 4.40e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.264 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.124α = 90
b = 142.124β = 90
c = 84.539γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
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)--

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description