4H80

Crystal structure of human ALDH3A1 with its isozyme selective inhibitor - N-[4-(4-methylsulfonyl-2-nitroanilino)phenyl]acetamide

• PDB DOI: https://doi.org/10.2210/pdb4H80/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-09-21 Released: 2013-12-25 
• Deposition Author(s): Hurley, T.D., Parajuli, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Kinetic and Structural Characterization of a Selective Inhibitor for Human ALDH3A1

Parajuli, B., Georgiadis, T., Fishel, M.L., Hurley, T.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 420.76 kDa 
• Atom Count: 28,414 
• Modelled Residue Count: 3,570 
• Deposited Residue Count: 3,752 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase, dimeric NADP-preferring	A, B, C, D, E, F, G, H	469	Homo sapiens	Mutation(s): 1  Gene Names: ALDH3, ALDH3A1 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
04T	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	N-(4-{[4-(methylsulfonyl)-2-nitrophenyl]amino}phenyl)acetamide C15 H15 N3 O5 S JXZXJHWSQKISBZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
04T	BindingDB:  4H80	Ki: 4700 (nM) from 1 assay(s)
		IC50: 1.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.106	α = 112.38
b = 95.38	β = 91.68
c = 117.228	γ = 90.99

Software Package:

Software Name	Purpose
HKL-3000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Hurley, T.D., Parajuli, B.

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description