Crystal structure of human ALDH2 modified with the beta-elimination product of Aldi-3; 1-(4-ethylbenzene)prop-2-en-1-one

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Discovery of a novel class of covalent inhibitor for aldehyde dehydrogenases.

Khanna, M.Chen, C.H.Kimble-Hill, A.Parajuli, B.Perez-Miller, S.Baskaran, S.Kim, J.Dria, K.Vasiliou, V.Mochly-Rosen, D.Hurley, T.D.

(2011) J Biol Chem 286: 43486-43494

  • DOI: https://doi.org/10.1074/jbc.M111.293597
  • Primary Citation of Related Structures:  
    3SZ9, 3SZA, 3SZB

  • PubMed Abstract: 

    Human aldehyde dehydrogenases (ALDHs) comprise a family of 17 homologous enzymes that metabolize different biogenic and exogenic aldehydes. To date, there are relatively few general ALDH inhibitors that can be used to probe the contribution of this class of enzymes to particular metabolic pathways. Here, we report the discovery of a general class of ALDH inhibitors with a common mechanism of action. The combined data from kinetic studies, mass spectrometric measurements, and crystallographic analyses demonstrate that these inhibitors undergo an enzyme-mediated β-elimination reaction generating a vinyl ketone intermediate that covalently modifies the active site cysteine residue present in these enzymes. The studies described here can provide the basis for rational approach to design ALDH isoenzyme-specific inhibitors as research tools and perhaps as drugs, to address diseases such as cancer where increased ALDH activity is associated with a cellular phenotype.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.

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
500Homo 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 I3E

Download Ideal Coordinates CCD File 
CA [auth C]
DB [auth G]
HA [auth D]
KB [auth H]
MA [auth E]
CA [auth C],
DB [auth G],
HA [auth D],
KB [auth H],
MA [auth E],
N [auth A],
S [auth B],
XA [auth F]
C11 H14 O
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CB [auth G]
GA [auth D]
HB [auth H]
AA [auth C],
BA [auth C],
CB [auth G],
GA [auth D],
HB [auth H],
IB [auth H],
JB [auth H],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
R [auth B],
SA [auth F],
T [auth C],
TA [auth F],
UA [auth F],
VA [auth F],
WA [auth F],
Y [auth C],
YA [auth F],
Z [auth C]
C2 H6 O2
Query on GAI

Download Ideal Coordinates CCD File 
AB [auth G]
BB [auth G]
DA [auth C]
FA [auth D]
FB [auth H]
AB [auth G],
BB [auth G],
DA [auth C],
FA [auth D],
FB [auth H],
GB [auth H],
J [auth A],
JA [auth E],
K [auth A],
NA [auth E],
OA [auth F],
P [auth B],
Q [auth B],
QA [auth F],
RA [auth F],
V [auth C],
W [auth C],
X [auth C]
C H5 N3
Query on NA

Download Ideal Coordinates CCD File 
EA [auth D]
EB [auth H]
I [auth A]
IA [auth E]
O [auth B]
EA [auth D],
EB [auth H],
I [auth A],
IA [auth E],
O [auth B],
PA [auth F],
U [auth C],
ZA [auth G]
Binding Affinity Annotations 
IDSourceBinding Affinity
I3E PDBBind:  3SZ9 IC50: 5400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.522α = 90
b = 151.052β = 90
c = 177.021γ = 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: 2011-11-02
    Type: Initial release
  • Version 1.1: 2011-12-28
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Database references
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description