1US0

Human Aldose Reductase in complex with NADP+ and the inhibitor IDD594 at 0.66 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.66 Å
  • R-Value Free: 0.103 
  • R-Value Observed: 0.094 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ultrahigh Resolution Drug Design I: Details of Interactions in Human Aldose Reductase-Inhibitor Complex at 0.66 A.

Howard, E.I.Sanishvili, R.Cachau, R.E.Mitschler, A.Chevrier, B.Barth, P.Lamour, V.Van Zandt, M.Sibley, E.Bon, C.Moras, D.Schneider, T.R.Joachimiak, A.Podjarny, A.

(2004) Proteins 55: 792

  • DOI: 10.1002/prot.20015
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The first subatomic resolution structure of a 36 kDa protein [aldose reductase (AR)] is presented. AR was cocrystallized at pH 5.0 with its cofactor NADP+ and inhibitor IDD 594, a therapeutic candidate for the treatment of diabetic complications. X-r ...

    The first subatomic resolution structure of a 36 kDa protein [aldose reductase (AR)] is presented. AR was cocrystallized at pH 5.0 with its cofactor NADP+ and inhibitor IDD 594, a therapeutic candidate for the treatment of diabetic complications. X-ray diffraction data were collected up to 0.62 A resolution and treated up to 0.66 A resolution. Anisotropic refinement followed by a blocked matrix inversion produced low standard deviations (<0.005 A). The model was very well ordered overall (CA atoms' mean B factor is 5.5 A2). The model and the electron-density maps revealed fine features, such as H-atoms, bond densities, and significant deviations from standard stereochemistry. Other features, such as networks of hydrogen bonds (H bonds), a large number of multiple conformations, and solvent structure were also better defined. Most of the atoms in the active site region were extremely well ordered (mean B approximately 3 A2), leading to the identification of the protonation states of the residues involved in catalysis. The electrostatic interactions of the inhibitor's charged carboxylate head with the catalytic residues and the charged coenzyme NADP+ explained the inhibitor's noncompetitive character. Furthermore, a short contact involving the IDD 594 bromine atom explained the selectivity profile of the inhibitor, important feature to avoid toxic effects. The presented structure and the details revealed are instrumental for better understanding of the inhibition mechanism of AR by IDD 594, and hence, for the rational drug design of future inhibitors. This work demonstrates the capabilities of subatomic resolution experiments and stimulates further developments of methods allowing the use of the full potential of these experiments.


    Organizational Affiliation

    Laboratoire de Génomique et de Biologie Structurales, UMR 7104 du CNRS, IGBMC, Illkirch, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALDOSE REDUCTASE
A
316Homo sapiensMutation(s): 0 
Gene Names: AKR1B1ALDR1ALR2
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
LDT
Query on LDT

Download CCD File 
A
IDD594
C16 H12 Br F2 N O3 S
JCZUIWYXULSXSW-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LDTΔG:  40.900001525878906   kJ/mol  BindingDB
LDTΔG:  31.299999237060547   kJ/mol  BindingDB
LDTΔG:  31.5   kJ/mol  BindingDB
LDTIC50:  3   nM  BindingDB
LDTΔH:  46.20000076293945   kJ/mol  BindingDB
LDT-TΔS:  7.989999771118164   kJ/mol  BindingDB
LDT-TΔS:  22.59000015258789   kJ/mol  BindingDB
LDTΔG:  38.70000076293945   kJ/mol  BindingDB
LDTIC50:  30   nM  Binding MOAD
LDT-TΔS:  14.6899995803833   kJ/mol  BindingDB
LDTIC50:  30   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.66 Å
  • R-Value Free: 0.103 
  • R-Value Observed: 0.094 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.28α = 90
b = 66.59β = 92.4
c = 47.26γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXLphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-07
    Type: Initial release
  • Version 1.1: 2014-03-05
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2019-05-22
    Changes: Advisory, Data collection, Other, Refinement description