8RRJ | pdb_00008rrj

The structural basis of aldo-keto reductase 1C3 inhibition by 17alpha-picolyl and 17(E)-picolinylidene androstane derivatives


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.221 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The structural basis of aldo-keto reductase 1C3 inhibition by 17 alpha-picolyl and 17( E )-picolinylidene androstane derivatives.

Plavsa-Puz, J.J.Brynda, J.Ajdukovic, J.J.Bekic, S.Celic, A.Rezacova, P.Skerlova, J.Petri, E.

(2025) J Enzyme Inhib Med Chem 40: 2551979-2551979

  • DOI: https://doi.org/10.1080/14756366.2025.2551979
  • Primary Citation of Related Structures:  
    8RRJ

  • PubMed Abstract: 

    Human aldo-keto reductase 1C3 (AKR1C3) is a steroid modifying enzyme involved in cancer progression. Here, A-ring modified 17α-picolyl and 17( E )-picolinylidene androstane derivatives are shown to inhibit AKR1C3 activity in vitro . None of the androstane derivatives have off-target affinity for the androgen receptor, based on a fluorescence assay in yeast cells. The X-ray structure of AKR1C3 in complex with the strongest inhibitor, a 17α-picolyl androstane with a C3-oxime modification, was determined at 1.7 Å resolution. Based on this crystal structure and molecular docking, inhibition of AKR1C3 by the 17α-picolyl or 17( E )-picolinylidene derivatives depends on interactions between the C3 modification and the NADP + cofactor, while the C17α-picolyl or C17-picolinylidene group anchors the inhibitor to AKR1C3. Because one AKR1C3 inhibitor identified here was also previously reported to inhibit CYP17, it may be possible for future researchers to design dual AKR1C3/CYP17 inhibitors based on a steroid scaffold for potential treatment of advanced prostate cancers.


  • Organizational Affiliation
    • Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia.

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
326Homo sapiensMutation(s): 0 
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 3 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
A1H2U (Subject of Investigation/LOI)
Query on A1H2U

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
(3~{Z},8~{R},9~{S},10~{R},13~{S},14~{S},17~{R})-3-hydroxyimino-10,13-dimethyl-17-(pyridin-2-ylmethyl)-2,6,7,8,9,11,12,14,15,16-decahydro-1~{H}-cyclopenta[a]phenanthren-17-ol
C25 H34 N2 O2
OXDFJJOYBOXYDL-DUXFNIGSSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.221 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.17α = 77.71
b = 53.52β = 85.61
c = 75.62γ = 76.06
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government451-03-47/2023-01/200125
Other government142-451-3463/2023-01
European Union (EU)European UnionLX22NPO5102

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references
  • Version 1.2: 2025-09-17
    Changes: Database references