2NVD

Human Aldose Reductase complexed with novel naphtho[1,2-d]isothiazole acetic acid derivative (2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evidence for a novel binding site conformer of aldose reductase in ligand-bound state

Steuber, H.Zentgraf, M.La Motta, C.Sartini, S.Heine, A.Klebe, G.

(2007) J.Mol.Biol. 369: 186-197

  • DOI: 10.1016/j.jmb.2007.03.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human aldose reductase (ALR2) has evolved as a promising therapeutic target for the treatment of diabetic long-term complications. The binding site of this enzyme possesses two main subpockets: the catalytic anion-binding site and the hydrophobic spe ...

    Human aldose reductase (ALR2) has evolved as a promising therapeutic target for the treatment of diabetic long-term complications. The binding site of this enzyme possesses two main subpockets: the catalytic anion-binding site and the hydrophobic specificity pocket. The latter can be observed in the open or closed state, depending on the bound ligand. Thus, it exhibits a pronounced capability for induced-fit adaptations, whereas the catalytic pocket exhibits rigid properties throughout all known crystal structures. Here, we determined two ALR2 crystal structures at 1.55 and 1.65 A resolution, each complexed with an inhibitor of the recently described naphtho[1,2-d]isothiazole acetic acid series. In contrast to the original design hypothesis based on the binding mode of tolrestat (1), both inhibitors leave the specificity pocket in the closed state. Unexpectedly, the more potent ligand (2) extends the catalytic pocket by opening a novel subpocket. Access to this novel subpocket is mainly attributed to the rotation of an indole moiety of Trp 20 by about 35 degrees . The newly formed subpocket provides accommodation of the naphthyl portion of the ligand. The second inhibitor, 3, differs from 2 only by an extended glycolic ester functionality added to one of its carboxylic groups. However, despite this slight structural modification, the binding mode of 3 differs dramatically from that of the first inhibitor, but provokes less pronounced induced-fit adaptations of the binding cavity. Thus, a novel binding site conformation has been identified in a region where previous complex structures suggested only low adaptability of the binding pocket. Furthermore, the two ligand complexes represent an impressive example of how the slight change of a chemically extended side-chain at a given ligand scaffold can result in a dramatically altered binding mode. In addition, our study emphasizes the importance of crystal structure analysis for the translation of affinity data into structure-activity relationships.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldose reductase
A
316Homo sapiensMutation(s): 0 
Gene Names: AKR1B1 (ALDR1)
EC: 1.1.1.21
Find proteins for P15121 (Homo sapiens)
Go to Gene View: AKR1B1
Go to UniProtKB:  P15121
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ITB
Query on ITB

Download SDF File 
Download CCD File 
A
2-(CARBOXYMETHYL)-1-OXO-1,2-DIHYDRONAPHTHO[1,2-D]ISOTHIAZOLE-4-CARBOXYLIC ACID 3,3-DIOXIDE
2-CARBOXYMETHYL-1,3,3-TRIOXO-1,2-DIHYDRONAPHTHO[1,2-D]ISOTHIAZOLE-4-CARBOXYLIC ACID
C14 H9 N O7 S
ZTJGXDGAXGWOGR-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ITBIC50: 140 nM (99) BINDINGDB
ITBIC50: 550 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.130 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.390α = 90.00
b = 66.640β = 91.88
c = 47.140γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data scaling
SHELXmodel building
CNSphasing
SHELXL-97refinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance