4KWF

Crystal Structure Analysis of ALDH2+ALDiB33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Development of selective inhibitors for aldehyde dehydrogenases based on substituted indole-2,3-diones.

Kimble-Hill, A.C.Parajuli, B.Chen, C.H.Mochly-Rosen, D.Hurley, T.D.

(2014) J.Med.Chem. 57: 714-722

  • DOI: 10.1021/jm401377v
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aldehyde dehydrogenases (ALDH) participate in multiple metabolic pathways and have been indicated to play a role in several cancerous disease states. Our laboratory is interested in developing novel and selective ALDH inhibitors. We looked to further ...

    Aldehyde dehydrogenases (ALDH) participate in multiple metabolic pathways and have been indicated to play a role in several cancerous disease states. Our laboratory is interested in developing novel and selective ALDH inhibitors. We looked to further work recently published by developing a class of isoenzyme-selective inhibitors using similar indole-2,3-diones that exhibit differential inhibition of ALDH1A1, ALDH2, and ALDH3A1. Kinetic and X-ray crystallography data suggest that these inhibitors are competitive against aldehyde binding, forming direct interactions with active-site cysteine residues. The selectivity is precise in that these compounds appear to interact directly with the catalytic nucleophile, Cys243, in ALDH3A1 but not in ALDH2. In ALDH2, the 3-keto group is surrounded by the adjacent Cys301/303. Surprisingly, the orientation of the interaction changes depending on the nature of the substitutions on the basic indole ring structure and correlates well with the observed structure-activity relationships for each ALDH isoenzyme.


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Indiana University School of Medicine , MS4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldehyde dehydrogenase, mitochondrial
A, B, C, D, E, F, G, H
494Homo sapiensMutation(s): 0 
Gene Names: ALDH2 (ALDM)
EC: 1.2.1.3
Find proteins for P05091 (Homo sapiens)
Go to Gene View: ALDH2
Go to UniProtKB:  P05091
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
3AK
Query on 3AK

Download SDF File 
Download CCD File 
A, B, E, H
1-benzyl-1H-indole-2,3-dione
C15 H11 N O2
SIISFRLGYDVIRG-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C, E, F, H
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
GAI
Query on GAI

Download SDF File 
Download CCD File 
A, B, C, D, F, G, H
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3AKKi: 15000 - 34000 nM (100) BINDINGDB
3AKIC50: 82000 nM (100) BINDINGDB
3AKIC50: 82000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 102.293α = 90.00
b = 177.092β = 94.39
c = 102.551γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACphasing
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
DENZOdata reduction
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description