4KWG

Crystal Structure Analysis of ALDH2+ALDiB13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Development of selective inhibitors for aldehyde dehydrogenases based on substituted indole-2,3-diones.

Kimble-Hill, A.C.Parajuli, B.Chen, C.H.Mochly-Rosen, D.Hurley, T.D.

(2014) J Med Chem 57: 714-722

  • DOI: 10.1021/jm401377v
  • Primary Citation of Related Structures:  
    4KWF, 4KWG

  • PubMed Abstract: 
  • Aldehyde dehydrogenases (ALDH) participate in multiple metabolic pathways and have been indicated to play a role in several cancerous disease states. Our laboratory is interested in developing novel and selective ALDH inhibitors. We looked to further work recently published by developing a class of isoenzyme-selective inhibitors using similar indole-2,3-diones that exhibit differential inhibition of ALDH1A1, ALDH2, and ALDH3A1 ...

    Aldehyde dehydrogenases (ALDH) participate in multiple metabolic pathways and have been indicated to play a role in several cancerous disease states. Our laboratory is interested in developing novel and selective ALDH inhibitors. We looked to further work recently published by developing a class of isoenzyme-selective inhibitors using similar indole-2,3-diones that exhibit differential inhibition of ALDH1A1, ALDH2, and ALDH3A1. Kinetic and X-ray crystallography data suggest that these inhibitors are competitive against aldehyde binding, forming direct interactions with active-site cysteine residues. The selectivity is precise in that these compounds appear to interact directly with the catalytic nucleophile, Cys243, in ALDH3A1 but not in ALDH2. In ALDH2, the 3-keto group is surrounded by the adjacent Cys301/303. Surprisingly, the orientation of the interaction changes depending on the nature of the substitutions on the basic indole ring structure and correlates well with the observed structure-activity relationships for each ALDH isoenzyme.


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Indiana University School of Medicine , MS4053, 635 Barnhill Drive, Indianapolis, Indiana 46202, United States.



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
494Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05091
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2AK
Query on 2AK

Download Ideal Coordinates CCD File 
DA [auth H],
I [auth A]
7-bromo-5-methyl-1H-indole-2,3-dione
C9 H6 Br N O2
NPDJRIGMWAQKTQ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
FA [auth H],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
FA [auth H],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
W [auth E],
Y [auth F],
Z [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
GAI
Query on GAI

Download Ideal Coordinates CCD File 
AA [auth F],
CA [auth G],
GA [auth H],
M [auth A],
Q [auth B],
AA [auth F],
CA [auth G],
GA [auth H],
M [auth A],
Q [auth B],
S [auth C],
U [auth D]
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth G],
EA [auth H],
J [auth A],
N [auth B],
R [auth C],
BA [auth G],
EA [auth H],
J [auth A],
N [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2AK BindingDB:  4KWG Ki: min: 1000, max: 2200 (nM) from 2 assay(s)
IC50: 2400 (nM) from 1 assay(s)
Binding MOAD:  4KWG Ki: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.506α = 90
b = 176.193β = 94.92
c = 101.546γ = 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: 2014-04-09
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description