3RX3

Crystal Structure of Human Aldose Reductase Complexed with Sulindac

• PDB DOI: https://doi.org/10.2210/pdb3RX3/pdb

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


• Deposited: 2011-05-10 Released: 2011-11-30 
• Deposition Author(s): Zheng, X., Chen, J., Luo, H., Hu, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.201 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 

Starting Model: experimental

Literature

The molecular basis for inhibition of sulindac and its metabolites towards human aldose reductase.

Zheng, X., Zhang, L., Zhai, J., Chen, Y., Luo, H., Hu, X.

(2012) FEBS Lett 586: 55-59

• PubMed: 22155003 
• DOI: https://doi.org/10.1016/j.febslet.2011.11.023
• Primary Citation of Related Structures:  
  3RX2, 3RX3, 3RX4, 3S3G


• PubMed Abstract: 
  

  Sulindac (SLD) exhibits both the highest inhibitory activity towards human aldose reductase (AR) among popular non-steroidal anti-inflammatory drugs and clear beneficial clinical effects on Type 2 diabetes. However, the molecular basis for these properties is unclear. Here, we report that SLD and its pharmacologically active/inactive metabolites, SLD sulfide and SLD sulfone, are equally effective as un-competitive inhibitors of AR in vitro. Crystallographic analysis reveals that π-π stacking favored by the distinct scaffold of SLDs is pivotal to their high AR inhibitory activities. These results also suggest that SLD sulfone could be a potent lead compound for AR inhibition in vivo.

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Organizational Affiliation: 

School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China. [e-mail]

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: 39.17 kDa 
• Atom Count: 3,053 
• Modelled Residue Count: 318 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase	A	336	Homo sapiens	Mutation(s): 0  Gene Names: AKR1B1, ALDR1 EC: 1.1.1.21 (PDB Primary Data), 1.1.1.372 (UniProt), 1.1.1.300 (UniProt), 1.1.1.54 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P15121 (Homo sapiens) Explore P15121  Go to UniProtKB:  P15121
PHAROS:  P15121 GTEx:  ENSG00000085662

Small Molecules

Ligands 2 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
SUZ	C [auth A]	[(1Z)-5-fluoro-2-methyl-1-{4-[methylsulfinyl]benzylidene}-1H-inden-3-yl]acetic acid C20 H17 F O3 S MLKXDPUZXIRXEP-LQVWSKNFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SUZ	BindingDB:  3RX3	IC50: 293 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.201 
• R-Value Work: 0.150 
• R-Value Observed: 0.153 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.153	α = 90
b = 66.726	β = 92.1
c = 49.319	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
PHENIX	refinement
CrysalisPro	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-30 
Deposition Author(s): Zheng, X., Chen, J., Luo, H., Hu, X.

Revision History  

• Version 1.0: 2011-11-30
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description