4DBW

Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 (AKR1C3) in complex with NADP+ and 2'-desmethyl-indomethacin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.802 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Development of potent and selective indomethacin analogues for the inhibition of AKR1C3 (Type 5 17 beta-hydroxysteroid dehydrogenase/prostaglandin F synthase) in castrate-resistant prostate cancer.

Liedtke, A.J.Adeniji, A.O.Chen, M.Byrns, M.C.Jin, Y.Christianson, D.W.Marnett, L.J.Penning, T.M.

(2013) J.Med.Chem. 56: 2429-2446

  • DOI: 10.1021/jm3017656

  • PubMed Abstract: 
  • Castrate-resistant prostate cancer (CRPC) is a fatal, metastatic form of prostate cancer. CRPC is characterized by reactivation of the androgen axis due to changes in androgen receptor signaling and/or adaptive intratumoral androgen biosynthesis. AKR ...

    Castrate-resistant prostate cancer (CRPC) is a fatal, metastatic form of prostate cancer. CRPC is characterized by reactivation of the androgen axis due to changes in androgen receptor signaling and/or adaptive intratumoral androgen biosynthesis. AKR1C3 is upregulated in CRPC where it catalyzes the formation of potent androgens. This makes AKR1C3 a target for the treatment of CRPC. AKR1C3 inhibitors should not inhibit AKR1C1/AKR1C2, which inactivate 5α-dihydrotestosterone. Indomethacin, used to inhibit cyclooxygenase, also inhibits AKR1C3 and displays selectivity over AKR1C1/AKR1C2. Parallel synthetic strategies were used to generate libraries of indomethacin analogues, which exhibit reduced cyclooxygenase inhibitory activity but retain AKR1C3 inhibitory potency and selectivity. The lead compounds inhibited AKR1C3 with nanomolar potency, displayed >100-fold selectivity over AKR1C1/AKR1C2, and blocked testosterone formation in LNCaP-AKR1C3 cells. The AKR1C3·NADP(+)·2'-des-methyl-indomethacin crystal structure was determined, and it revealed a unique inhibitor binding mode. The compounds reported are promising agents for the development of therapeutics for CRPC.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldo-keto reductase family 1 member C3
A, B
323Homo sapiensMutation(s): 0 
Gene Names: AKR1C3 (DDH1, HSD17B5, KIAA0119, PGFS)
EC: 1.-.-.-
Find proteins for P42330 (Homo sapiens)
Go to Gene View: AKR1C3
Go to UniProtKB:  P42330
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
511
Query on 511

Download SDF File 
Download CCD File 
A, B
[1-(4-chlorobenzoyl)-5-methoxy-1H-indol-3-yl]acetic acid
2'-desmethyl-indomethacin
C18 H14 Cl N O4
DHEMTWWLRLOBKI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
511IC50: 1 - 960 nM (99) BINDINGDB
511IC50: 100 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.802 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.178 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 47.346α = 74.30
b = 49.089β = 87.04
c = 83.445γ = 69.95
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description