3SZ9

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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 ...

    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: 
    • Alda-1 is an agonist and chemical chaperone for the common human aldehyde dehydrogenase 2 variant
      Perez-Miller, S., Younus, H., Vanam, R., Chen, C.-H., Mochly-Rosen, D., Hurley, T.D.
      (2010) Nat Struct Mol Biol 17: 159
    • Activation of Aldehyde Dehydrogenase-2 Reduces Ischemic Damage to the Heart
      Chen, C.-H., Budas, G.R., Churchill, E.N., Disatnik, M.-H., Hurley, T.D., Mochly-Rosen, D.
      (2008) Science 321: 1493

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aldehyde dehydrogenase, mitochondrialA, B, C, D, E, F, G, H500Homo sapiensMutation(s): 0 
Gene Names: ALDH2ALDM
EC: 1.2.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05091 (Homo sapiens)
Explore P05091 
Go to UniProtKB:  P05091
PHAROS:  P05091
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I3E (Subject of Investigation/LOI)
Query on I3E

Download Ideal Coordinates CCD File 
CA [auth C], DB [auth G], HA [auth D], KB [auth H], MA [auth E], N [auth A], S [auth B], XA [auth F]1-(4-ethylphenyl)propan-1-one
C11 H14 O
VGQRIILEZYZAOE-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CB [auth G] , GA [auth D] , HB [auth H] , IB [auth H] , JB [auth H] , KA [auth E] , 
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]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
GAI
Query on GAI

Download Ideal Coordinates CCD File 
AB [auth G] , BB [auth G] , DA [auth C] , FA [auth D] , FB [auth H] , GB [auth H] , J [auth A] , JA [auth E] , 
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]
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



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