8HUB

AMP deaminase 2 in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The discovery of 3,3-dimethyl-1,2,3,4-tetrahydroquinoxaline-1-carboxamides as AMPD2 inhibitors with a novel mechanism of action.

Kitao, Y.Saito, T.Watanabe, S.Ohe, Y.Takahashi, K.Akaki, T.Adachi, T.Doi, S.Yamanaka, K.Murai, Y.Oba, M.Suzuki, T.

(2023) Bioorg Med Chem Lett 80: 129110-129110

  • DOI: https://doi.org/10.1016/j.bmcl.2022.129110
  • Primary Citation of Related Structures:  
    8HU6, 8HUB

  • PubMed Abstract: 

    AMP deaminase 2 (AMPD2) has been thought to play an important role in energy homeostasis and immuno-oncology, while selective AMPD2 inhibitors are highly demanded to clarify the physiological function of AMPD2. In this report, we describe selective AMPD2 inhibitors inducing allosteric modulation. Based on hypothesis that compounds that exhibit increased inhibition by preincubation would cause conformational change of the enzyme, starting from HTS hit compound 4, we discovered compound 8 through the SAR study. From X-ray structural information of 8, this chemical series has a novel mechanism of action that changes the substrate pocket to prevent AMP from binding. Further elaboration of compound 8 led to the tool compound 21 which exhibited potent inhibitory activity of AMPD2 in ex vivo evaluation of mouse liver.


  • Organizational Affiliation

    Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan; Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan. Electronic address: yuki.kitao@jt.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AMP deaminase 2
A, B, C, D
678Homo sapiensMutation(s): 0 
Gene Names: AMPD2
EC: 3.5.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q01433 (Homo sapiens)
Explore Q01433 
Go to UniProtKB:  Q01433
PHAROS:  Q01433
GTEx:  ENSG00000116337 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01433
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.516α = 90
b = 162.533β = 90
c = 289.758γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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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: 2023-01-18
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references