Crystal structure of human AKR1B1 complexed with NADP+ and compound 37

Experimental Data Snapshot

  • Resolution: 0.94 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

Starting Model: experimental
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Design, synthesis, structure-activity relationships and X-ray structural studies of novel 1-oxopyrimido[4,5-c]quinoline-2-acetic acid derivatives as selective and potent inhibitors of human aldose reductase.

Crespo, I.Gimenez-Dejoz, J.Porte, S.Cousido-Siah, A.Mitschler, A.Podjarny, A.Pratsinis, H.Kletsas, D.Pares, X.Ruiz, F.X.Metwally, K.Farres, J.

(2018) Eur J Med Chem 152: 160-174

  • DOI: https://doi.org/10.1016/j.ejmech.2018.04.015
  • Primary Citation of Related Structures:  
    5OU0, 5OUJ, 5OUK

  • PubMed Abstract: 

    Human aldose reductase (AKR1B1, AR) is a key enzyme of the polyol pathway, catalyzing the reduction of glucose to sorbitol at high glucose concentrations, as those found in diabetic condition. Indeed, AKR1B1 overexpression is related to diabetes secondary complications and, in some cases, with cancer. For many years, research has been focused on finding new AKR1B1 inhibitors (ARIs) to overcome these diseases. Despite the efforts, most of the new drug candidates failed because of their poor pharmacokinetic properties and/or unacceptable side effects. Here we report the synthesis of a series of 1-oxopyrimido[4,5-c]quinoline-2-acetic acid derivatives as novel ARIs. IC 50 assays and X-ray crystallographic studies proved that these compounds are promising hits for further drug development, with high potency and selectivity against AKR1B1. Based on the determined X-ray structures with hit-to-lead compounds, we designed and synthesized a second series that yielded lead compound 68 (K i app vs. AKR1B1 = 73 nM). These compounds are related to the previously reported 2-aminopyrimido[4,5-c]quinolin-1(2H)-ones, which exhibit antimitotic activity. Regardless of their similarity, the 2-amino compounds are unable to inhibit AKR1B1 while the 2-acetic acid derivatives are not cytotoxic against fibrosarcoma HT-1080 cells. Thus, the replacement of the amino group by an acetic acid moiety changes their biological activity, improving their potency as ARIs.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldose reductase316Homo sapiensMutation(s): 0 
Gene Names: AKR1B1ALDR1
UniProt & NIH Common Fund Data Resources
Find proteins for P15121 (Homo sapiens)
Explore P15121 
Go to UniProtKB:  P15121
GTEx:  ENSG00000085662 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15121
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAP

Download Ideal Coordinates CCD File 
C21 H28 N7 O17 P3
AV5 (Subject of Investigation/LOI)
Query on AV5

Download Ideal Coordinates CCD File 
C [auth A]2-[5-(4-chlorophenyl)-3-methyl-1-oxidanylidene-pyrimido[4,5-c]quinolin-2-yl]ethanoic acid
C20 H14 Cl N3 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 0.94 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.758α = 76.45
b = 46.771β = 67.76
c = 47.157γ = 78.18
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description