2PDK

Human aldose reductase mutant L301M complexed with sorbinil.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 

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
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldose reductase
A
316Homo 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)
Find proteins for P15121 (Homo sapiens)
Go to UniProtKB:  P15121
NIH Common Fund Data Resources
PHAROS  P15121
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
SBI
Query on SBI

Download CCD File 
A
SORBINIL
C11 H9 F N2 O3
LXANPKRCLVQAOG-NSHDSACASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SBIIC50:  1000   nM  BindingDB
SBI-TΔS:  9.800000190734863   kJ/mol  BindingDB
SBIΔG:  29.600000381469727   kJ/mol  BindingDB
SBIIC50:  29   nM  BindingDB
SBIIC50:  9000   nM  BindingDB
SBIIC50:  8000   nM  BindingDB
SBIΔH:  35.400001525878906   kJ/mol  BindingDB
SBI-TΔS:  13.890000343322754   kJ/mol  BindingDB
SBIIC50:  500   nM  BindingDB
SBIIC50:  550   nM  BindingDB
SBIIC50:  150   nM  BindingDB
SBIΔG:  40.900001525878906   kJ/mol  BindingDB
SBIIC50:  100   nM  BindingDB
SBIΔG:  38.900001525878906   kJ/mol  BindingDB
SBIΔG:  37.900001525878906   kJ/mol  BindingDB
SBIIC50:  700   nM  BindingDB
SBIΔG:  31.5   kJ/mol  BindingDB
SBIΔG:  34.5   kJ/mol  BindingDB
SBIIC50:  70   nM  BindingDB
SBIIC50:  73   nM  BindingDB
SBIIC50:  910   nM  BindingDB
SBI-TΔS:  14.6899995803833   kJ/mol  BindingDB
SBIIC50:  4700   nM  BindingDB
SBIΔG:  41.5   kJ/mol  BindingDB
SBIΔG:  35.400001525878906   kJ/mol  BindingDB
SBIIC50:  2000   nM  BindingDB
SBIIC50:  7200   nM  BindingDB
SBIIC50:  2000   nM  BindingDB
SBIIC50:  20   nM  BindingDB
SBI-TΔS:  29.709999084472656   kJ/mol  BindingDB
SBIΔG:  38.70000076293945   kJ/mol  BindingDB
SBIIC50:  3600   nM  BindingDB
SBIIC50:  17   nM  BindingDB
SBIΔG:  42.20000076293945   kJ/mol  BindingDB
SBI-TΔS:  12.489999771118164   kJ/mol  BindingDB
SBIIC50:  620   nM  BindingDB
SBIIC50:  67   nM  BindingDB
SBIIC50:  70   nM  BindingDB
SBIIC50:  650   nM  BindingDB
SBIIC50:  20000   nM  BindingDB
SBIIC50:  4400   nM  BindingDB
SBIΔG:  31.299999237060547   kJ/mol  BindingDB
SBIIC50:  500   nM  BindingDB
SBIIC50:  3140   nM  BindingDB
SBI-TΔS:  36.88999938964844   kJ/mol  BindingDB
SBIIC50:  3040   nM  BindingDB
SBIΔH:  46.20000076293945   kJ/mol  BindingDB
SBIIC50:  918.5999755859375   nM  BindingDB
SBI-TΔS:  7.989999771118164   kJ/mol  BindingDB
SBI-TΔS:  5.659999847412109   kJ/mol  BindingDB
SBIIC50:  990   nM  BindingDB
SBIIC50:  2000   nM  BindingDB
SBIIC50:  900   nM  BindingDB
SBIIC50:  1850   nM  BindingDB
SBIIC50:  1560   nM  BindingDB
SBIIC50:  180   nM  BindingDB
SBIIC50:  249   nM  BindingDB
SBIIC50:  250   nM  BindingDB
SBIIC50:  1500   nM  BindingDB
SBIIC50:  1410   nM  BindingDB
SBIIC50:  190   nM  BindingDB
SBIIC50:  200   nM  BindingDB
SBIIC50:  1100   nM  BindingDB
SBI-TΔS:  22.59000015258789   kJ/mol  BindingDB
SBIIC50:  1000   nM  BindingDB
SBIIC50:  120   nM  BindingDB
SBIIC50:  140   nM  BindingDB
SBIIC50:  430   nM  BindingDB
SBIΔH:  54   kJ/mol  BindingDB
SBIIC50:  170   nM  BindingDB
SBIIC50:  230   nM  BindingDB
SBIIC50:  280   nM  BindingDB
SBIKd:  270   nM  Binding MOAD
SBIIC50:  249   nM  BindingDB
SBIIC50:  250   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.42α = 90
b = 66.62β = 91.86
c = 47.37γ = 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 

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