9FFD

STRUCTURE OF ALDO-KETO REDUCTASE 1C3 (AKR1C3) IN COMPLEX WITH AN INHIBITOR MEDS765


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

AI Based Discovery of a New AKR1C3 Inhibitor for Anticancer Applications.

Pippione, A.C.Vigato, C.Tucciarello, C.Hussain, S.Salladini, E.Truong, H.H.Henriksen, N.M.Vanzetti, G.Giordano, G.Zonari, D.Mirza, O.A.Frydenvang, K.Pignochino, Y.Oliaro-Bosso, S.Boschi, D.Lolli, M.L.

(2024) ACS Med Chem Lett 15: 1269-1278

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00150
  • Primary Citation of Related Structures:  
    9FFD

  • PubMed Abstract: 

    AKR1C3 is an upregulated enzyme in prostate and other cancers; in addition to regulating hormone synthesis, this enzyme is thought to play a role in the aggressiveness of tumors and in the defense against drugs. We here used an unbiased method to discover new potent AKR1C3 inhibitors: through an AI-based virtual drug screen, compound 4 was identified as a potent and selective enzymatic inhibitor able to translate this activity into a pronounced antiproliferative effect in the 22RV1 prostate cancer cell model. As other known AKR1C3 inhibitors, compound 4 determined a significantly increased activity of abiraterone, a drug approved for advanced prostate cancer. Compound 4 also showed a synergic effect with doxorubicin in osteosarcoma cell lines; specifically, the effect is correlated with AKR1C3 expression. In this research work, therefore, the use of AI allowed the identification of a new structure as an AKR1C3 inhibitor and its potential to enhance the effect of chemotherapeutics.


  • Organizational Affiliation

    Department of Science and Drug Technology, University of Turin, via Pietro Giuria 9, 10125 Turin, Italy.


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
323Homo sapiensMutation(s): 1 
Gene Names: AKR1C3DDH1HSD17B5KIAA0119PGFS
EC: 1.1.1 (PDB Primary Data), 1.1.1.210 (PDB Primary Data), 1.1.1.53 (PDB Primary Data), 1.1.1.62 (PDB Primary Data), 1.1.1.357 (PDB Primary Data), 1.1.1.188 (PDB Primary Data), 1.1.1.239 (PDB Primary Data), 1.1.1.64 (PDB Primary Data)
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
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
A1ICG (Subject of Investigation/LOI)
Query on A1ICG

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
~{N}-(4-bromanyl-2-methyl-phenyl)-2-[methyl-[(8-methyl-7-oxidanyl-2-oxidanylidene-chromen-4-yl)methyl]amino]ethanamide
C21 H21 Br N2 O4
VRVRPZJTYVPJNC-UHFFFAOYSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
I [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.228α = 74.12
b = 48.791β = 85.35
c = 83.314γ = 69.6
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

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: 2024-08-21
    Type: Initial release
  • Version 1.1: 2024-08-28
    Changes: Database references