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 
  • R-Value Observed: 0.180 

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
  • Structures With Same Primary Citation

  • 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 Pharmacol 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 dehydrogenaseA, B469Homo sapiensMutation(s): 1 
Gene Names: ALDH3A1ALDH3
EC: 1.2.1.5
Find proteins for P30838 (Homo sapiens)
Explore P30838 
Go to UniProtKB:  P30838
NIH Common Fund Data Resources
PHAROS  P30838
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I1E
Query on I1E

Download CCD File 
A, B
1-phenylpropan-1-one
C9 H10 O
KRIOVPPHQSLHCZ-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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

Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-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 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.377α = 90
b = 85.727β = 90
c = 169.555γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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