7VBT

Crystal structure of RIOK2 in complex with CQ211


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of 8-(6-Methoxypyridin-3-yl)-1-(4-(piperazin-1-yl)-3-(trifluoromethyl)phenyl)-1,5-dihydro- 4H -[1,2,3]triazolo[4,5- c ]quinolin-4-one (CQ211) as a Highly Potent and Selective RIOK2 Inhibitor.

Ouyang, Y.Si, H.Zhu, C.Zhong, L.Ma, H.Li, Z.Xiong, H.Liu, T.Liu, Z.Zhang, Z.Zhang, Z.M.Cai, Q.

(2022) J Med Chem 65: 7833-7842

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00271
  • Primary Citation of Related Structures:  
    7VBT

  • PubMed Abstract: 

    RIOK2 is an atypical kinase implicated in multiple human cancers. Although recent studies establish the role of RIOK2 in ribosome maturation and cell cycle progression, its biological functions remain poorly elucidated, hindering the potential to explore RIOK2 as a therapeutic target. Here, we report the discovery of CQ211 , the most potent and selective RIOK2 inhibitor reported so far. CQ211 displays a high binding affinity ( K d = 6.1 nM) and shows excellent selectivity to RIOK2 in both enzymatic and cellular studies. It also exhibits potent proliferation inhibition activity against multiple cancer cell lines and demonstrates promising in vivo efficacy in mouse xenograft models. The crystal structure of RIOK2- CQ211 sheds light on the molecular mechanism of inhibition and informs the subsequent optimization. The study provides a cell-active chemical probe for verifying RIOK2 functions, which may also serve as a leading molecule in the development of therapeutic RIOK2 inhibitors.


  • Organizational Affiliation

    College of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou 510530, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase RIO2
A, B
319Homo sapiensMutation(s): 0 
Gene Names: RIOK2RIO2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVS4 (Homo sapiens)
Explore Q9BVS4 
Go to UniProtKB:  Q9BVS4
PHAROS:  Q9BVS4
GTEx:  ENSG00000058729 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BVS4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5ZH (Subject of Investigation/LOI)
Query on 5ZH

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
8-(6-methoxypyridin-3-yl)-1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]-5H-[1,2,3]triazolo[4,5-c]quinolin-4-one
C26 H22 F3 N7 O2
RGHLRMNPUGUZEY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.517α = 90
b = 93.605β = 90
c = 110.965γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description