1EF3

FIDARESTAT BOUND TO HUMAN ALDOSE REDUCTASE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

A potent aldose reductase inhibitor, (2S,4S)-6-fluoro-2', 5'-dioxospiro[chroman-4,4'-imidazolidine]-2-carboxamide (Fidarestat): its absolute configuration and interactions with the aldose reductase by X-ray crystallography.

Oka, M., Matsumoto, Y., Sugiyama, S., Tsuruta, N., Matsushima, M.

(2000) J Med Chem 43: 2479-2483

  • DOI: 10.1021/jm990502r
  • Primary Citation of Related Structures:  
    1EF3

  • PubMed Abstract: 

    • The absolute configuration of the aldose reductase (AR) inhibitor, (+)-(2S,4S)-6-fluoro-2',5'-dioxospiro¿chroman-4, 4'-imidazolidine-2-carboxamide (fidarestat), was established indirectly by single-crystal X-ray analysis of (+)-(2S, 4S)-8-bromo-6-fluoro-2',5'-dioxospiro¿chroman-4, 4'-imidazolidine-2-carboxylic acid (1) ...

    The absolute configuration of the aldose reductase (AR) inhibitor, (+)-(2S,4S)-6-fluoro-2',5'-dioxospiro¿chroman-4, 4'-imidazolidine-2-carboxamide (fidarestat), was established indirectly by single-crystal X-ray analysis of (+)-(2S, 4S)-8-bromo-6-fluoro-2',5'-dioxospiro¿chroman-4, 4'-imidazolidine-2-carboxylic acid (1). The crystal structure of human AR complexed with fidarestat was determined, and the specific inhibition activity was discussed on the basis of the three-dimensional interactions between them. The structure clarified that fidarestat was located in the active site by hydrophilic and hydrophobic interactions and that the carbamoyl group of fidarestat was a very effective substituent for affinity to AR and for selectivity between AR and aldehyde reductase (AHR). Explanations for the differences between the observed activities of fidarestat and its stereoisomer 2 were suggested by computer modeling.

    Organizational Affiliation: 

    Rational Drug Design Laboratories, 4-1-1, Misato, Matsukawa-machi, Fukushima 960-1242, Japan. m_oka@mb6.skk-net.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALDOSE REDUCTASEA, B315Homo sapiensMutation(s): 0 
Gene Names: AKR1B1, ALDR1, ALR2
EC: 1.1.1.21 (PDB Primary Data), 1.1.1.300 (UniProt), 1.1.1.372 (UniProt), 1.1.1.54 (UniProt)
Find proteins for P15121 (Homo sapiens)
Explore P15121 
Go to UniProtKB:  P15121
NIH Common Fund Data Resources
PHAROS:  P15121
GTEx:  ENSG00000085662
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
 C [auth A], E [auth B]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N		 Ligand Interaction
FID
Query on FID
Download Ideal Coordinates CCD File 
 D [auth A], F [auth B](2S,4S)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN-4,4'-IMIDAZOLIDINE]-2',5'-DIONE
C12 H10 F N3 O4
WAAPEIZFCHNLKK-UFBFGSQYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FIDΔG:  38   kJ/mol  BindingDB
FIDΔH:  29.899999618530273   kJ/mol  BindingDB
FID-TΔS:  5.659999847412109   kJ/mol  BindingDB
FIDKd:  16   nM  BindingDB
FIDΔG:  38.900001525878906   kJ/mol  BindingDB
FID-TΔS:  28.790000915527344   kJ/mol  BindingDB
FID-TΔS:  9.800000190734863   kJ/mol  BindingDB
FIDIC50:  9   nM  BindingDB
FIDIC50:  35   nM  BindingDB
FIDΔG:  29.600000381469727   kJ/mol  BindingDB
FIDIC50:  35   nM  BindingDB
FIDΔG:  29.299999237060547   kJ/mol  BindingDB
FIDΔG:  37.900001525878906   kJ/mol  BindingDB
FIDΔG:  35.400001525878906   kJ/mol  BindingDB
FIDIC50:  29   nM  BindingDB
FID-TΔS:  0.6000000238418579   kJ/mol  BindingDB
FIDΔG:  42.70000076293945   kJ/mol  BindingDB
FID-TΔS:  19.399999618530273   kJ/mol  BindingDB
FIDΔH:  35.400001525878906   kJ/mol  BindingDB
FID-TΔS:  29.709999084472656   kJ/mol  BindingDB
FIDIC50:  30   nM  BindingDB
FIDΔG:  46.70000076293945   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.14α = 90
b = 62.56β = 101.6
c = 118.99γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation