Crystal Structure Analysis of ALDH2+ALDiB33

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 

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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: https://doi.org/10.1021/jm401377v
  • Primary Citation of Related Structures:  
    4KWF, 4KWG

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase, mitochondrial
A, B, C, D, E
A, B, C, D, E, F, G, H
494Homo sapiensMutation(s): 0 
Gene Names: ALDH2ALDM
UniProt & NIH Common Fund Data Resources
Find proteins for P05091 (Homo sapiens)
Explore P05091 
Go to UniProtKB:  P05091
PHAROS:  P05091
GTEx:  ENSG00000111275 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05091
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3AK

Download Ideal Coordinates CCD File 
FA [auth H],
I [auth A],
N [auth B],
W [auth E]
C15 H11 N O2
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth F]
HA [auth H]
K [auth A]
L [auth A]
R [auth C]
BA [auth F],
HA [auth H],
K [auth A],
L [auth A],
R [auth C],
S [auth C],
Y [auth E],
Z [auth E]
C2 H6 O2
Query on GAI

Download Ideal Coordinates CCD File 
CA [auth F]
EA [auth G]
IA [auth H]
M [auth A]
P [auth B]
CA [auth F],
EA [auth G],
IA [auth H],
M [auth A],
P [auth B],
T [auth C],
V [auth D]
C H5 N3
Query on NA

Download Ideal Coordinates CCD File 
AA [auth F]
DA [auth G]
GA [auth H]
J [auth A]
O [auth B]
AA [auth F],
DA [auth G],
GA [auth H],
J [auth A],
O [auth B],
Q [auth C],
U [auth D],
X [auth E]
Binding Affinity Annotations 
IDSourceBinding Affinity
3AK Binding MOAD:  4KWF Ki: 1.50e+4 (nM) from 1 assay(s)
BindingDB:  4KWF Ki: min: 1.50e+4, max: 3.40e+4 (nM) from 2 assay(s)
IC50: 8.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.293α = 90
b = 177.092β = 94.39
c = 102.551γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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