3SZB

Crystal structure of human ALDH3A1 modified with the beta-elimination product of Aldi-1; 1-phenyl- 2-propen-1-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1074/jbc.M111.293597
  • Primary Citation of Related Structures:  

  • 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 c ...

    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.


    Related Citations: 
    • A point mutation produced a class 3 aldehyde dehydrogenase with increased protective ability against the killing effect of cyclophosphamide
      Ho, K.K.,Mukhopadhyay, A.,Li, Y.F.,Mukhopadhyay, S.,Weiner, H.
      (2008) BIOCHEM.PHARM. 76: 690
    • The first structure of an aldehyde dehydrogenase reveals novel interactions between NAD and the Rossmann Fold
      Liu, Z.J.,Sun, Y.J.,Rose, J.,Chung, Y.J.,Hsiao, C.D.,Chang, W.R.,Kuo, I.,Perozich, J.,Lindahl, R.,Hempel, J.,Wang, B.C.
      (1997) Nat.Struct.Mol.Biol. 4: 317


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldehyde dehydrogenase
A, B
469Homo sapiensMutation(s): 0 
Gene Names: ALDH3A1 (ALDH3)
EC: 1.2.1.5
Find proteins for P30838 (Homo sapiens)
Go to Gene View: ALDH3A1
Go to UniProtKB:  P30838
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
I1E
Query on I1E

Download SDF File 
Download CCD File 
A, B
1-phenylpropan-1-one
1-phenyl-2-propen-1-one, bound form
C9 H10 O
KRIOVPPHQSLHCZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
I1EIC50: 12000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.377α = 90.00
b = 85.727β = 90.00
c = 169.555γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
AMoREphasing
HKL-3000data reduction
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000data collection
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2011-12-28
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Database references