3T42

Human aldose reductase in complex with a nitrile-containing IDD inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Electrostatic Fields near the Active Site of Human Aldose Reductase: 2. New Inhibitors and Complications Caused by Hydrogen Bonds.

Xu, L.Cohen, A.E.Boxer, S.G.

(2011) Biochemistry 50: 8311-8322

  • DOI: 10.1021/bi200930f

  • PubMed Abstract: 
  • Vibrational Stark effect spectroscopy was used to measure electrostatic fields in the hydrophobic region of the active site of human aldose reductase (hALR2). A new nitrile-containing inhibitor was designed and synthesized, and the X-ray structure of ...

    Vibrational Stark effect spectroscopy was used to measure electrostatic fields in the hydrophobic region of the active site of human aldose reductase (hALR2). A new nitrile-containing inhibitor was designed and synthesized, and the X-ray structure of its complex, along with cofactor NADP(+), with wild-type hALR2 was determined at 1.3 Å resolution. The nitrile is found to be in the proximity of T113, consistent with a hydrogen bond interaction. Two vibrational absorption peaks were observed at room temperature in the nitrile region when the inhibitor binds to wild-type hALR2, indicating that the nitrile probe experiences two different microenvironments, and these could be empirically separated into a hydrogen-bonded and non-hydrogen-bonded population by comparison with the T113A mutant, in which a hydrogen bond to the nitrile is not present. Classical molecular dynamics simulations based on the structure predict a double-peak distribution in protein electric fields projected along the nitrile probe. The interpretation of these two peaks as a hydrogen bond formation-dissociation process between the probe nitrile group and a nearby amino acid side chain is used to explain the observation of two IR bands, and the simulations were used to investigate the molecular details of this conformational change. Hydrogen bonding complicates the simplest analysis of vibrational frequency shifts as being due solely to electrostatic interactions through the vibrational Stark effect, and the consequences of this complication are discussed.


    Organizational Affiliation

    Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldose reductase
A
319Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-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
3T4
Query on 3T4

Download SDF File 
Download CCD File 
A
{5-chloro-2-[(4-cyano-3-nitrobenzyl)carbamoyl]phenoxy}acetic acid
C17 H12 Cl N3 O6
VTRDVRBVJGKWET-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3T4Ki: 107 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.151 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 39.858α = 76.35
b = 46.963β = 77.21
c = 46.907γ = 67.79
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release