2FZB

Human Aldose Reductase complexed with four tolrestat molecules at 1.5 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Expect the Unexpected or Caveat for Drug Designers: Multiple Structure Determinations Using Aldose Reductase Crystals Treated under Varying Soaking and Co-crystallisation Conditions.

Steuber, H.Zentgraf, M.Gerlach, C.Sotriffer, C.A.Heine, A.Klebe, G.

(2006) J Mol Biol 363: 174-187

  • DOI: 10.1016/j.jmb.2006.08.011
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In structure-based drug design, accurate crystal structure determination of protein-ligand complexes is of utmost importance in order to elucidate the binding characteristics of a putative lead to a given target. It is the starting point for further ...

    In structure-based drug design, accurate crystal structure determination of protein-ligand complexes is of utmost importance in order to elucidate the binding characteristics of a putative lead to a given target. It is the starting point for further design hypotheses to predict novel leads with improved properties. Often, crystal structure determination is regarded as ultimate proof for ligand binding providing detailed insight into the specific binding mode of the ligand to the protein. This widely accepted practise relies on the assumption that the crystal structure of a given protein-ligand complex is unique and independent of the protocol applied to produce the crystals. We present two examples indicating that this assumption is not generally given, even though the composition of the mother liquid for crystallisation was kept unchanged: Multiple crystal structure determinations of aldose reductase complexes obtained under varying crystallisation protocols concerning soaking and crystallisation exposure times were performed resulting in a total of 17 complete data sets and ten refined crystal structures, eight in complex with zopolrestat and two complexed with tolrestat. In the first example, a flip of a peptide bond is observed, obviously depending on the crystallisation protocol with respect to soaking and co-crystallisation conditions. This peptide flip is accompanied by a rupture of an H-bond formed to the bound ligand zopolrestat. The indicated enhanced local mobility of the complex is in agreement with the results of molecular dynamics simulations. As a second example, the aldose reductase-tolrestat complex is studied. Unexpectedly, two structures could be obtained: one with one, and a second with four inhibitor molecules bound to the protein. They are located in and near the binding pocket facilitated by crystal packing effects. Accommodation of the four ligand molecules is accompanied by pronounced shifts concerning two helices interacting with the additional ligands.


    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: ALDR1AKR1B1ALR2
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
TOL
Query on TOL

Download CCD File 
A
TOLRESTAT
C16 H14 F3 N O3 S
LUBHDINQXIHVLS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TOLIC50:  34   nM  BindingDB
TOLIC50:  35   nM  BindingDB
TOLIC50:  33   nM  BindingDB
TOLIC50:  1000   nM  BindingDB
TOLΔG:  29.299999237060547   kJ/mol  BindingDB
TOLΔG:  46.70000076293945   kJ/mol  BindingDB
TOL-TΔS:  19.399999618530273   kJ/mol  BindingDB
TOLΔG:  42.70000076293945   kJ/mol  BindingDB
TOLIC50:  950   nM  BindingDB
TOLIC50:  3   nM  BindingDB
TOLIC50:  50   nM  BindingDB
TOLIC50:  10   nM  BindingDB
TOLIC50:  47   nM  BindingDB
TOLΔH:  29.899999618530273   kJ/mol  BindingDB
TOL-TΔS:  28.790000915527344   kJ/mol  BindingDB
TOLIC50:  96   nM  BindingDB
TOLΔG:  38   kJ/mol  BindingDB
TOL-TΔS:  0.6000000238418579   kJ/mol  BindingDB
TOLIC50:  24   nM  BindingDB
TOLIC50:  400   nM  BindingDB
TOLIC50:  40   nM  BindingDB
TOLIC50:  15   nM  BindingDB
TOLIC50:  35   nM  BindingDB
TOLIC50:  16   nM  BindingDB
TOLIC50:  2   nM  BindingDB
TOLIC50:  540   nM  BindingDB
TOLIC50:  13   nM  BindingDB
TOLIC50:  1   nM  BindingDB
TOLIC50:  30   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.2α = 90
b = 68.1β = 92.84
c = 46.73γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
CrystalCleardata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance