4WEV

Crystal structure of human AKR1B10 complexed with NADP+ and sulindac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.453 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural analysis of sulindac as an inhibitor of aldose reductase and AKR1B10.

Cousido-Siah, A.Ruiz, F.X.Crespo, I.Porte, S.Mitschler, A.Pares, X.Podjarny, A.Farres, J.

(2015) Chem.Biol.Interact. 234: 290-296

  • DOI: 10.1016/j.cbi.2014.12.018

  • PubMed Abstract: 
  • Aldose reductase (AR, AKR1B1) and AKR1B10 are enzymes implicated in important pathologies (diabetes and cancer) and therefore they have been proposed as suitable targets for drug development. Sulindac is the metabolic precursor of the potent non-ster ...

    Aldose reductase (AR, AKR1B1) and AKR1B10 are enzymes implicated in important pathologies (diabetes and cancer) and therefore they have been proposed as suitable targets for drug development. Sulindac is the metabolic precursor of the potent non-steroidal anti-inflammatory drug (NSAID) sulindac sulfide, which suppresses prostaglandin production by inhibition of cyclooxygenases (COX). In addition, sulindac has been found to be one of the NSAIDs with higher antitumoral activity, presumably through COX inhibition. However, sulindac anticancer activity could be partially mediated through COX-independent mechanisms, including the participation of AR and AKR1B10. Previously, it had been shown that sulindac and sulindac sulfone were good AR inhibitors and the structure of the ternary complex with NADP(+) and sulindac was described (PDB ID 3U2C). In this work, we determined the three-dimensional structure of AKR1B10 with sulindac and established structure-activity relationships (SAR) of sulindac and their derivatives with AR and AKR1B10. The difference in the IC50 values for sulindac between AR (0.36 μM) and AKR1B10 (2.7 μM) might be explained by the different positioning and stacking interaction given by Phe122/Phe123, and by the presence of two buried and ordered water molecules in AKR1B10 but not in AR. Moreover, SAR analysis shows that the substitution of the sulfinyl group is structurally allowed in sulindac derivatives. Hence, sulindac and its derivatives emerge as lead compounds for the design of more potent and selective AR and AKR1B10 inhibitors.


    Organizational Affiliation

    Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire - Centre de Biologie Intégrative, CNRS, INSERM, UdS, 1 rue Laurent Fries, 67404 Illkirch Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldo-keto reductase family 1 member B10
X
316Homo sapiensMutation(s): 2 
Gene Names: AKR1B10 (AKR1B11)
EC: 1.1.1.300, 1.1.1.54
Find proteins for O60218 (Homo sapiens)
Go to Gene View: AKR1B10
Go to UniProtKB:  O60218
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

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

Download SDF File 
Download CCD File 
X
[(1Z)-5-fluoro-2-methyl-1-{4-[methylsulfinyl]benzylidene}-1H-inden-3-yl]acetic acid
SULINDAC
C20 H17 F O3 S
MLKXDPUZXIRXEP-LQVWSKNFSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
X
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
MLY
Query on MLY
X
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SUZIC50: 2690 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.453 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.188 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 78.848α = 90.00
b = 78.848β = 90.00
c = 50.127γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-05-13
    Type: Database references