3UWE

AKR1C3 complexed with 3-phenoxybenzoic acid

• PDB DOI: https://doi.org/10.2210/pdb3UWE/pdb

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


• Deposited: 2011-12-01 Released: 2012-04-04 
• Deposition Author(s): Jackson, V.J., Yosaatmadja, Y., Flanagan, J.U., Squire, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.214 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Structure of AKR1C3 with 3-phenoxybenzoic acid bound

Jackson, V.J., Yosaatmadja, Y., Flanagan, J.U., Squire, C.J.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 409-413

• PubMed: 22505408 
• DOI: https://doi.org/10.1107/S1744309112009049
• Primary Citation of Related Structures:  
  3UWE


• PubMed Abstract: 
  

  Aldo-keto reductase 1C3 (AKR1C3) is a human enzyme that catalyzes the NADPH-dependent reduction of steroids and prostaglandins. AKR1C3 overexpression is associated with the proliferation of hormone-dependent cancers, most notably breast and prostate cancers. Nonsteroidal anti-inflammatory drugs (NSAIDs) and their analogues are well characterized inhibitors of AKR1C3. Here, the X-ray crystal structure of 3-phenoxybenzoic acid in complex with AKR1C3 is presented. This structure provides useful information for the future development of new anticancer agents by structure-guided drug design.

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Organizational Affiliation: 

School of Biological Sciences, University of Auckland, Private Bag 92019, Victoria St. West, Auckland, New Zealand.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 39.2 kDa 
• Atom Count: 2,739 
• Modelled Residue Count: 314 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1 member C3	A	331	Homo sapiens	Mutation(s): 0  Gene Names: AKR1C3, DDH1, HSD17B5, KIAA0119, PGFS EC: 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	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
VJJ	C [auth A]	3-phenoxybenzoic acid C13 H10 O3 NXTDJHZGHOFSQG-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
VJJ	BindingDB:  3UWE	IC50: 680 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.214 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.473	α = 90
b = 64.699	β = 90
c = 96.959	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Jackson, V.J., Yosaatmadja, Y., Flanagan, J.U., Squire, C.J.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2014-03-05
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description