4FAM | pdb_00004fam

Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 5 in complex with 3-((3,4-dihydroisoquinolin-2(1H)-yl)sulfonyl)benzoic acid (17)

• PDB DOI: https://doi.org/10.2210/pdb4FAM/pdb

• Classification: oxidoreductase/oxidoreductase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-22 Released: 2012-10-10 
• Deposition Author(s): Turnbull, A.P., Jamieson, S.M.F., Brooke, D.G., Heinrich, D., Atwell, G.J., Silva, S., Hamilton, E.J., Rigoreau, L.J.M., Trivier, E., Soudy, C., Samlal, S.S., Owen, P.J., Schroeder, E., Raynham, T., Flanagan, J.U., Denny, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.218 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

3-(3,4-Dihydroisoquinolin-2(1H)-ylsulfonyl)benzoic acids; a New Class of Highly Potent and Selective Inhibitors of the Type 5 17-beta-hydroxysteroid Dehydrogenase AKR1C3

Jamieson, S.M., Brooke, D.G., Heinrich, D., Atwell, G.J., Silva, S., Hamilton, E.J., Turnbull, A.P., Rigoreau, L.J., Trivier, E., Soudy, C., Samlal, S.S., Owen, P.J., Schroeder, E., Raynham, T., Flanagan, J.U., Denny, W.A.

(2012) J Med Chem 55: 7746-7758

• PubMed: 22877157 
• DOI: https://doi.org/10.1021/jm3007867
• Primary Citation Related Structures: 
  4FA3, 4FAL, 4FAM


• PubMed Abstract: 
  

  A high-throughput screen identified 3-(3,4-dihydroisoquinolin-2(1H)-ylsulfonyl)benzoic acid as a novel, highly potent (low nM), and isoform-selective (1500-fold) inhibitor of aldo-keto reductase AKR1C3: a target of interest in both breast and prostate cancer. Crystal structure studies showed that the carboxylate group occupies the oxyanion hole in the enzyme, while the sulfonamide provides the correct twist to allow the dihydroisoquinoline to bind in an adjacent hydrophobic pocket. SAR studies around this lead showed that the positioning of the carboxylate was critical, although it could be substituted by acid isosteres and amides. Small substituents on the dihydroisoquinoline gave improvements in potency. A set of "reverse sulfonamides" showed a 12-fold preference for the R stereoisomer. The compounds showed good cellular potency, as measured by inhibition of AKR1C3 metabolism of a known dinitrobenzamide substrate, with a broad rank order between enzymic and cellular activity, but amide analogues were more effective than predicted by the cellular assay.

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Organizational Affiliation: 
• Auckland Cancer Society Research Centre, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 78.63 kDa 
• Atom Count: 5,732 
• Modeled Residue Count: 629 
• Deposited Residue Count: 662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1 member C3	A, B	331	Homo sapiens	Mutation(s): 0  Gene Names: AKR1C3, DDH1, HSD17B5, KIAA0119, PGFS EC: 1 (PDB Primary Data), 1.1.1.213 (PDB Primary Data), 1.1.1.112 (PDB Primary Data), 1.1.1.188 (PDB Primary Data), 1.1.1.63 (PDB Primary Data), 1.1.1.64 (PDB Primary Data), 1.3.1.20 (PDB Primary Data), 1.1.1.53 (UniProt), 1.1.1.62 (UniProt), 1.1.1.357 (UniProt), 1.1.1.239 (UniProt), 1.1.1 (UniProt), 1.1.1.210 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42330 (Homo sapiens) Explore P42330  Go to UniProtKB:  P42330
PHAROS:  P42330 GTEx:  ENSG00000196139

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], K [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
0SZ	D [auth A], L [auth B]	3-(3,4-dihydroisoquinolin-2(1H)-ylsulfonyl)benzoic acid C16 H15 N O4 S ZGVIUMKHTXKKOX-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0SZ	BindingDB:  4FAM	IC50: min: 13, max: 3.00e+4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.218 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.717	α = 90
b = 106.764	β = 103.11
c = 74.882	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Turnbull, A.P., Jamieson, S.M.F., Brooke, D.G., Heinrich, D., Atwell, G.J., Silva, S., Hamilton, E.J., Rigoreau, L.J.M., Trivier, E., Soudy, C., Samlal, S.S., Owen, P.J., Schroeder, E., Raynham, T., Flanagan, J.U., Denny, W.A.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description