3DN5

Aldose Reductase in complex with novel biarylic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Optimization of Aldose Reductase Inhibitors Originating from Virtual Screening

Eisenmann, M.Steuber, H.Zentgraf, M.Altenkamper, M.Ortmann, R.Perruchon, J.Klebe, G.Schlitzer, M.

(2009) Chemmedchem 4: 809-819

  • DOI: 10.1002/cmdc.200800410

  • PubMed Abstract: 
  • Diabetes mellitus is a universal health problem. The World Health Organization (WHO) estimates that 150 million people suffer from diabetes mellitus worldwide in 2005. Long-term complications are a serious problem in the treatment of diabetes, manife ...

    Diabetes mellitus is a universal health problem. The World Health Organization (WHO) estimates that 150 million people suffer from diabetes mellitus worldwide in 2005. Long-term complications are a serious problem in the treatment of diabetes, manifesting in macrovascular and microvascular complications. Sorbitol accumulation has been proposed to be an important factor in the development of microvascular complications such as nephropathy, neuropathy, retinopathy or cataract. Catalyzing the NADPH-dependent reduction of glucose to sorbitol, aldose reductase (ALR2) is an important target in the prevention of these complications. The development of novel aldose reductase inhibitors is expected to benefit strongly from a structure-based design approach. A virtual screening based on the ultrahigh-resolution crystal structure of the inhibitor IDD 594 in complex with human ALR2 identified two compounds with IC(50) values in the low micro- to submicromolar range. Based on the known interactions between the ligands and their binding pocket, we simplified the lead structures to give the minimal structural requirements and developed synthetic pathways from commercially available compounds. The newly synthesized compounds were assayed for their inhibition of ALR2, showing inhibitory activities down to the nanomolar range. Crystal structure analysis of the most potent derivative of our series revealed insights into the binding mode of the inhibitors.


    Organizational Affiliation

    Institut für Pharmazeutische Chemie, Philipps Universität 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, ALR2)
EC: 1.1.1.300, 1.1.1.372, 1.1.1.54
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
53N
Query on 53N

Download SDF File 
Download CCD File 
A
3-[5-(3-nitrophenyl)thiophen-2-yl]propanoic acid
C13 H11 N O4 S
IHKCOKRMJRDWAL-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 %)
53NIC50: 170 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.128 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.290α = 75.85
b = 47.155β = 67.48
c = 47.330γ = 76.59
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSphasing
HKL-2000data scaling
SHELXL-97refinement
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-07-01 
  • Released Date: 2009-04-07 
  • Deposition Author(s): Steuber, H., Klebe, G.

Revision History 

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance