3INL

Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, complexed with agonist Alda-1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

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: 159-164

  • DOI: 10.1038/nsmb.1737
  • Primary Citation of Related Structures:  
    3INJ, 3INL

  • PubMed Abstract: 

    • In approximately one billion people, a point mutation inactivates a key detoxifying enzyme, aldehyde dehydrogenase (ALDH2). This mitochondrial enzyme metabolizes toxic biogenic and environmental aldehydes, including the endogenously produced 4-hydroxynonenal (4HNE) and the environmental pollutant acrolein, and also bioactivates nitroglycerin ...

    In approximately one billion people, a point mutation inactivates a key detoxifying enzyme, aldehyde dehydrogenase (ALDH2). This mitochondrial enzyme metabolizes toxic biogenic and environmental aldehydes, including the endogenously produced 4-hydroxynonenal (4HNE) and the environmental pollutant acrolein, and also bioactivates nitroglycerin. ALDH2 is best known, however, for its role in ethanol metabolism. The accumulation of acetaldehyde following the consumption of even a single alcoholic beverage leads to the Asian alcohol-induced flushing syndrome in ALDH2*2 homozygotes. The ALDH2*2 allele is semidominant, and heterozygotic individuals show a similar but less severe phenotype. We recently identified a small molecule, Alda-1, that activates wild-type ALDH2 and restores near-wild-type activity to ALDH2*2. The structures of Alda-1 bound to ALDH2 and ALDH2*2 reveal how Alda-1 activates the wild-type enzyme and how it restores the activity of ALDH2*2 by acting as a structural chaperone.

    Related Citations: 
    • 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, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aldehyde dehydrogenase, mitochondrial
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
500Homo sapiensMutation(s): 2 
Gene Names: ALDH2, ALDM
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05091
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BXB
Query on BXB
Download Ideal Coordinates CCD File 
AA [auth C],
CB [auth H],
EA [auth D],
KA [auth E],
P [auth A],
AA [auth C],
CB [auth H],
EA [auth D],
KA [auth E],
P [auth A],
PA [auth F],
V [auth B],
XA [auth G]
N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide
C15 H11 Cl2 N O3
NMKJFZCBCIUYHI-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AB [auth H],
BB [auth H],
CA [auth D],
DA [auth D],
GA [auth E],
AB [auth H],
BB [auth H],
CA [auth D],
DA [auth D],
GA [auth E],
HA [auth E],
IA [auth E],
J [auth A],
JA [auth E],
K [auth A],
L [auth A],
LA [auth E],
M [auth A],
N [auth A],
NA [auth F],
O [auth A],
OA [auth F],
QA [auth F],
R [auth B],
RA [auth G],
S [auth B],
T [auth B],
TA [auth G],
U [auth B],
UA [auth G],
VA [auth G],
WA [auth G],
X [auth C],
Y [auth C],
Z [auth C],
ZA [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
BA [auth D],
FA [auth E],
I [auth A],
MA [auth F],
Q [auth B],
BA [auth D],
FA [auth E],
I [auth A],
MA [auth F],
Q [auth B],
SA [auth G],
W [auth C],
YA [auth H]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.121α = 90
b = 176.9β = 94.57
c = 102.323γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations