4L1O

Crystal structure of human ALDH3A1 with inhibitor 1-{[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]methyl}-1H-indole-2,3-dione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of indole-2,3-diones as novel class of inhibitors for ALDH isozymes.

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase
A, B
469Homo sapiensMutation(s): 1 
Gene Names: ALDH3ALDH3A1
EC: 1.2.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for P30838 (Homo sapiens)
Explore P30838 
Go to UniProtKB:  P30838
PHAROS:  P30838
GTEx:  ENSG00000108602 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30838
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1VL
Query on 1VL

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
(3S)-1-{[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]methyl}-3-hydroxy-1,3-dihydro-2H-indol-2-one
C21 H23 N3 O4
DHRNQNFHGGYALM-FQEVSTJZSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.257α = 90
b = 86.396β = 90
c = 170.225γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
AMoREphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Structure summary
  • Version 1.2: 2022-12-21
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-20
    Changes: Data collection, Refinement description