5L13 | pdb_00005l13

Structure of ALDH2 in complex with 2P3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.206 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 

Literature

Inhibition of the Aldehyde Dehydrogenase 1/2 Family by Psoralen and Coumarin Derivatives.

Buchman, C.D., Hurley, T.D.

(2017) J Med Chem 60: 2439-2455

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01825
  • Primary Citation Related Structures: 
    5L13, 5L2M, 5L2N, 5L2O

  • PubMed Abstract: 

    Aldehyde dehydrogenase 2 (ALDH2), one of 19 ALDH superfamily members, catalyzes the NAD + -dependent oxidation of aldehydes to their respective carboxylic acids. In this study, we further characterized the inhibition of four psoralen and coumarin derivatives toward ALDH2 and compared them to the ALDH2 inhibitor daidzin for selectivity against five ALDH1/2 isoenzymes. Compound 2 (K i = 19 nM) binds within the aldehyde-binding site of the free enzyme species of ALDH2. Thirty-three structural analogs were examined to develop a stronger SAR profile. Seven compounds maintained or improved upon the selectivity toward one of the five ALDH1/2 isoenzymes, including compound 36, a selective inhibitor for ALDH2 (K i = 2.4 μM), and compound 32, which was 10-fold selective for ALDH1A1 (K i = 1.2 μM) versus ALDH1A2. Further medicinal chemistry on the compounds' basic scaffold could enhance the potency and selectivity for ALDH1A1 or ALDH2 and generate chemical probes to examine the unique and overlapping functions of the ALDH1/2 isoenzymes.

    • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States.

Macromolecule Content 

  • Total Structure Weight: 455.56 kDa 
  • Atom Count: 32,476 
  • Modeled Residue Count: 3,953 
  • Deposited Residue Count: 4,136 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase, mitochondrial
A, B, C, D, E
A, B, C, D, E, F, G, H
517Homo sapiensMutation(s): 0 
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
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
6ZE

Query on 6ZE


Download:Ideal Coordinates CCD File
CA [auth D]
JA [auth E]
N [auth A]
OA [auth F]
S [auth B]
CA [auth D],
JA [auth E],
N [auth A],
OA [auth F],
S [auth B],
V [auth C],
WA [auth G],
ZA [auth H]
2,3,5-trimethyl-6-propyl-7H-furo[3,2-g][1]benzopyran-7-one
C17 H18 O3
ADGUVFJYVNRVPX-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
EA [auth E]
FA [auth E]
J [auth A]
K [auth A]
LA [auth F]
EA [auth E],
FA [auth E],
J [auth A],
K [auth A],
LA [auth F],
MA [auth F],
P [auth B],
Q [auth B],
QA [auth G],
RA [auth G],
SA [auth G],
X [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
GAI

Query on GAI


Download:Ideal Coordinates CCD File
AA [auth D]
BA [auth D]
GA [auth E]
HA [auth E]
IA [auth E]
AA [auth D],
BA [auth D],
GA [auth E],
HA [auth E],
IA [auth E],
L [auth A],
M [auth A],
NA [auth F],
R [auth B],
TA [auth G],
U [auth C],
UA [auth G],
VA [auth G],
Y [auth D],
YA [auth H],
Z [auth D]
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
NA

Query on NA


Download:Ideal Coordinates CCD File
DA [auth E]
I [auth A]
KA [auth F]
O [auth B]
PA [auth G]
DA [auth E],
I [auth A],
KA [auth F],
O [auth B],
PA [auth G],
T [auth C],
W [auth D],
XA [auth H]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6ZE BindingDB:  5L13 Ki: 19 (nM) from 1 assay(s)
IC50: 110 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.206 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.412α = 90
b = 127.049β = 90
c = 294.847γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)United StatesR01-AA018123

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-06
    Changes: Data collection, Database references, Derived calculations