3SZ9 | pdb_00003sz9

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 (Depositor), 0.159 (DCC) 
  • R-Value Work: 
    0.174 (Depositor) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3SZ9

Ligand Structure Quality Assessment 


This is version 1.5 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 Biological Chem 286: 43486-43494

  • DOI: https://doi.org/10.1074/jbc.M111.293597
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 439.85 kDa 
  • Atom Count: 33,400 
  • Modeled Residue Count: 3,953 
  • Deposited Residue Count: 4,000 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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
GTEx:  ENSG00000111275 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05091
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I3E

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]
1-(4-ethylphenyl)propan-1-one
C11 H14 O
VGQRIILEZYZAOE-UHFFFAOYSA-N
EDO

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]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
GAI

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]
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
NA

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]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.226 (Depositor), 0.159 (DCC) 
  • R-Value Work:  0.174 (Depositor) 
  • R-Value Observed: 0.176 (Depositor) 
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
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary