7C7H

Crystal structures of AKR1C3 ternary complex with NADP+ and the chromene derivative 2l

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

  • Deposited: 2020-05-25 Released: 2020-09-23 
  • Deposition Author(s): Irie, K., Toyooka, N., Endo, S.
  • Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development of Novel AKR1C3 Inhibitors as New Potential Treatment for Castration-Resistant Prostate Cancer.

Endo, S.Oguri, H.Segawa, J.Kawai, M.Hu, D.Xia, S.Okada, T.Irie, K.Fujii, S.Gouda, H.Iguchi, K.Matsukawa, T.Fujimoto, N.Nakayama, T.Toyooka, N.Matsunaga, T.Ikari, A.

(2020) J Med Chem 63: 10396-10411

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00939
  • Primary Citation of Related Structures:  
    7C7F, 7C7G, 7C7H

  • PubMed Abstract: 

    Aldo-keto reductase (AKR) 1C3 catalyzes the synthesis of active androgens that promote the progression of prostate cancer. AKR1C3 also contributes to androgen-independent cell proliferation and survival through the metabolism of prostaglandins and reactive aldehydes. Because of its elevation in castration-resistant prostate cancer (CRPC) tissues, AKR1C3 is a promising therapeutic target for CRPC. In this study, we found a novel potent AKR1C3 inhibitor, N -(4-fluorophenyl)-8-hydroxy-2-imino-2 H -chromene-3-carboxamide ( 2d ), and synthesized its derivatives with IC 50 values of 25-56 nM and >220-fold selectivity over other AKRs (1C1, 1C2, and 1C4). The structural factors for the inhibitory potency were elucidated by crystallographic study of AKR1C3 complexes with 2j and 2l . The inhibitors suppressed proliferation of prostate cancer 22Rv1 and PC3 cells through both androgen-dependent and androgen-independent mechanisms. Additionally, 2j and 2l prevented prostate tumor growth in a xenograft mouse model. Furthermore, the inhibitors significantly augmented apoptotic cell death induced by anti-CRPC drugs (abiraterone or enzalutamide).


  • Organizational Affiliation

    Laboratory of Biochemistry, Gifu Pharmaceutical University, Gifu 501-1196, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldo-keto reductase family 1 member C3
A, B
325Homo sapiensMutation(s): 0 
Gene Names: AKR1C3DDH1HSD17B5KIAA0119PGFS
EC: 1.3.1.20
UniProt & NIH Common Fund Data Resources
Find proteins for P42330 (Homo sapiens)
Explore P42330 
Go to UniProtKB:  P42330
PHAROS:  P42330
GTEx:  ENSG00000196139 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42330
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
FJU Binding MOAD:  7C7H IC50: 34 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.121α = 77.254
b = 52.314β = 86.161
c = 76.683γ = 77.639
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17K11151
Japan Society for the Promotion of Science (JSPS)JapanJP26460149
Japan Agency for Medical Research and Development (AMED)JapanJP17lm0203002

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description