2PD9

Human aldose reductase mutant V47I complexed with fidarestat.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Merging the binding sites of aldose and aldehyde reductase for detection of inhibitor selectivity-determining features.

Steuber, H.Heine, A.Podjarny, A.Klebe, G.

(2008) J Mol Biol 379: 991-1016

  • DOI: 10.1016/j.jmb.2008.03.063
  • Primary Citation of Related Structures:  
    2PD9, 2PDC, 2PDB, 2PD5, 2PDY, 2PDX, 2PDW, 2PDM, 2PDL, 2PDK

  • PubMed Abstract: 
  • Inhibition of human aldose reductase (ALR2) evolved as a promising therapeutic concept to prevent late complications of diabetes. As well as appropriate affinity and bioavailability, putative inhibitors should possess a high level of selectivity for ALR2 over the related aldehyde reductase (ALR1) ...

    Inhibition of human aldose reductase (ALR2) evolved as a promising therapeutic concept to prevent late complications of diabetes. As well as appropriate affinity and bioavailability, putative inhibitors should possess a high level of selectivity for ALR2 over the related aldehyde reductase (ALR1). We investigated the selectivity-determining features by gradually mapping the residues deviating between the binding pockets of ALR1 and ALR2 into the ALR2 binding pocket. The resulting mutational constructs of ALR2 (eight point mutations and one double mutant) were probed for their influence towards ligand selectivity by X-ray structure analysis of the corresponding complexes and isothermal titration calorimetry (ITC). The binding properties of these mutants were evaluated using a ligand set of zopolrestat, a related uracil derivative, IDD388, IDD393, sorbinil, fidarestat and tolrestat. Our study revealed induced-fit adaptations within the mutated binding site as an essential prerequisite for ligand accommodation related to the selectivity discrimination of the ligands. However, our study also highlights the limits of the present understanding of protein-ligand interactions. Interestingly, binding site mutations not involved in any direct interaction to the ligands in various cases show significant effects towards their binding thermodynamics. Furthermore, our results suggest the binding site residues deviating between ALR1 and ALR2 influence ligand affinity in a complex interplay, presumably involving changes of dynamic properties and differences of the solvation/desolvation balance upon ligand binding.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aldose reductaseA316Homo sapiensMutation(s): 1 
Gene Names: ALR2AKR1B1ALDR1
EC: 1.1.1.21 (PDB Primary Data), 1.1.1.300 (UniProt), 1.1.1.372 (UniProt), 1.1.1.54 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P15121 (Homo sapiens)
Explore P15121 
Go to UniProtKB:  P15121
PHAROS:  P15121
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
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
FID
Query on FID

Download Ideal Coordinates CCD File 
C [auth A](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 %)
FIDIC50:  35   nM  BindingDB
FIDΔG:  42.70000076293945   kJ/mol  BindingDB
FID-TΔS:  28.790000915527344   kJ/mol  BindingDB
FIDΔG:  38.900001525878906   kJ/mol  BindingDB
FIDΔG:  37.900001525878906   kJ/mol  BindingDB
FID-TΔS:  19.399999618530273   kJ/mol  BindingDB
FIDIC50:  9   nM  BindingDB
FID-TΔS:  29.709999084472656   kJ/mol  BindingDB
FIDIC50:  35   nM  BindingDB
FIDΔG:  29.600000381469727   kJ/mol  BindingDB
FID-TΔS:  9.800000190734863   kJ/mol  BindingDB
FIDΔG:  35.400001525878906   kJ/mol  BindingDB
FIDIC50:  30   nM  BindingDB
FIDΔH:  35.400001525878906   kJ/mol  BindingDB
FIDKd:  8.300000190734863   nM  Binding MOAD
FIDΔH:  29.899999618530273   kJ/mol  BindingDB
FID-TΔS:  5.659999847412109   kJ/mol  BindingDB
FID-TΔS:  0.6000000238418579   kJ/mol  BindingDB
FIDIC50:  29   nM  BindingDB
FIDKd:  16   nM  BindingDB
FIDΔG:  29.299999237060547   kJ/mol  BindingDB
FIDΔG:  46.70000076293945   kJ/mol  BindingDB
FIDΔG:  38   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.42α = 90
b = 66.91β = 92.11
c = 47.31γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance