1EKO

PIG ALDOSE REDUCTASE COMPLEXED WITH IDD384 INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The structure of human aldose reductase bound to the inhibitor IDD384.

Calderone, V.Chevrier, B.Van Zandt, M.Lamour, V.Howard, E.Poterszman, A.Barth, P.Mitschler, A.Lu, J.Dvornik, D.M.Klebe, G.Kraemer, O.Moorman, A.R.Moras, D.Podjarny, A.

(2000) Acta Crystallogr D Biol Crystallogr 56: 536-540

  • DOI: 10.1107/s0907444900002341
  • Primary Citation of Related Structures:  
    1EKO, 1EL3

  • PubMed Abstract: 
  • The crystallographic structure of the complex between human aldose reductase (AR2) and one of its inhibitors, IDD384, has been solved at 1.7 A resolution from crystals obtained at pH 5.0. This structure shows that the binding of the inhibitor's hydrophilic head to the catalytic residues Tyr48 and His110 differs from that found previously with porcine AR2 ...

    The crystallographic structure of the complex between human aldose reductase (AR2) and one of its inhibitors, IDD384, has been solved at 1.7 A resolution from crystals obtained at pH 5.0. This structure shows that the binding of the inhibitor's hydrophilic head to the catalytic residues Tyr48 and His110 differs from that found previously with porcine AR2. The difference is attributed to a change in the protonation state of the inhibitor (pK(a) = 4.52) when soaked with crystals of human (at pH 5.0) or pig lens AR2 (at pH 6.2). This work demonstrates how strongly the detailed binding of the inhibitor's polar head depends on its protonation state.


    Related Citations: 
    • Binding of Aldose Reductase Inhibitors: Correlation of Crystallographic and Mass Spectrometric Studies
      Rogniaux, H., Van Dorsselaer, A., Barth, P., Biellmann, J.F., Barbanton, J., van Zandt, M., Chevrier, B., Howard, E., Mitschler, A., Potier, N., Urzhumtseva, L., Moras, D., Podjarny, A.
      (1999) J Am Soc Mass Spectrom 10: 635

    Organizational Affiliation

    UPR de Biologie Structurale 9004, IGBMC, CNRS/INSERM/ULP, 1 Rue Laurent Fries, BP 163, 67404 Illkirch, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALDOSE REDUCTASEA315Sus scrofaMutation(s): 1 
Gene Names: AKR1B1ALR2
EC: 1.1.1.21 (PDB Primary Data), 1.1.1.300 (UniProt), 1.1.1.372 (UniProt), 1.1.1.54 (UniProt)
UniProt
Find proteins for P80276 (Sus scrofa)
Explore P80276 
Go to UniProtKB:  P80276
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
I84 (Subject of Investigation/LOI)
Query on I84

Download Ideal Coordinates CCD File 
C [auth A][2,6-DIMETHYL-4-(2-O-TOLYL-ACETYLAMINO)-BENZENESULFONYL]-GLYCINE
C19 H22 N2 O5 S
CJKKMQCZOLCXAM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AYA
Query on AYA
AL-PEPTIDE LINKINGC5 H9 N O3ALA
Binding Affinity Annotations 
IDSourceBinding Affinity
I84 BindingDB:  1EKO IC50: 108 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.81α = 90
b = 68.81β = 90
c = 154.77γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
AUTOMARdata reduction
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2000-03-09 
  • Released Date: 2000-05-10 
  • Deposition Author(s): Podjarny, A.

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-10
    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: 2017-10-04
    Changes: Refinement description