2AGT

Aldose Reductase Mutant Leu 300 Pro complexed with Fidarestat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Factorizing Selectivity Determinants of Inhibitor Binding toward Aldose and Aldehyde Reductases: Structural and Thermodynamic Properties of the Aldose Reductase Mutant Leu300Pro-Fidarestat Complex

Petrova, T.Steuber, H.Hazemann, I.Cousido-Siah, A.Mitschler, A.Chung, R.Oka, M.Klebe, G.El-Kabbani, O.Joachimiak, A.Podjarny, A.

(2005) J Med Chem 48: 5659-5665

  • DOI: https://doi.org/10.1021/jm050424+
  • Primary Citation of Related Structures:  
    2AGT

  • PubMed Abstract: 

    Structure of the Leu300Pro mutant of human aldose reductase (ALR2) in complex with the inhibitor fidarestat is determined. Comparison with the hALR2-fidarestat complex and the porcine aldehyde reductase (ALR1)-fidarestat complex indicates that the hydrogen bond between the Leu300 amino group of the wild-type and the exocyclic amide group of the inhibitor is the key determinant for the specificity of fidarestat for ALR2 over ALR1. Thermodynamic data also suggest an enthalpic contribution as the predominant difference in the binding energy between the aldose reductase mutant and the wild-type. An additional selectivity-determining feature is the difference in the interaction between the inhibitor and the side chain of Trp219, ordered in the present structure but disordered (corresponding Trp220) in the ALR1-fidarestat complex. Thus, the hydrogen bond ( approximately 7 kJ/mol) corresponds to a 23-fold difference in inhibitor potency while the differences in the interactions between Trp219(ALR2) and fidarestat and between Trp220(ALR1) and fidarestat can account for an additional 10-fold difference in potency.


  • Organizational Affiliation

    Laboratoire de Génomique et de Biologie Structurales, UMR 7104 du CNRS, IGBMC, 1 Rue Laurent Fries, B.P. 10142, 67404 Illkirch, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldose reductase319Homo sapiensMutation(s): 1 
Gene Names: AKR1B1ALDR1
EC: 1.1.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for P15121 (Homo sapiens)
Explore P15121 
Go to UniProtKB:  P15121
PHAROS:  P15121
GTEx:  ENSG00000085662 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15121
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
FID
Query on FID

Download Ideal Coordinates CCD File 
D [auth A](2S,4S)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN-4,4'-IMIDAZOLIDINE]-2',5'-DIONE
C12 H10 F N3 O4
WAAPEIZFCHNLKK-UFBFGSQYSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
FID BindingDB:  2AGT Kd: 16 (nM) from 1 assay(s)
IC50: min: 9, max: 35 (nM) from 5 assay(s)
-TΔS: min: -9.80e+0, max: 29.71 (kJ/mol) from 6 assay(s)
ΔH: min: -3.54e+1, max: -2.99e+1 (kJ/mol) from 2 assay(s)
ΔG: min: -4.67e+1, max: -2.93e+1 (kJ/mol) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.129 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.106 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.118α = 90
b = 66.724β = 92.79
c = 47.092γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description