4X0T | pdb_00004x0t

Structure ALDH7A1 inactivated by 4-diethylaminobenzaldehyde and complexed with NAD+

• PDB DOI: https://doi.org/10.2210/pdb4X0T/pdb

• Classification: oxidoreductase/oxidoreductase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-23 Released: 2015-01-14 
• Deposition Author(s): Luo, M., Tanner, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.235 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Diethylaminobenzaldehyde Is a Covalent, Irreversible Inactivator of ALDH7A1.

Luo, M., Gates, K.S., Henzl, M.T., Tanner, J.J.

(2015) ACS Chem Biol 10: 693-697

• PubMed: 25554827 
• DOI: https://doi.org/10.1021/cb500977q
• Primary Citation Related Structures: 
  4X0T, 4X0U


• PubMed Abstract: 
  

  There is growing interest in aldehyde dehydrogenases (ALDHs) because of their overexpression in cancer stem cells and the ability to mediate resistance to cancer drugs. Here, we report the first crystal structure of an aldehyde dehydrogenase complexed with the inhibitor 4-diethylaminobenzaldehyde (DEAB). Contrary to the widely held belief that DEAB is a reversible inhibitor of ALDHs, we show that DEAB irreversibly inactivates ALDH7A1 via formation of a stable, covalent acyl-enzyme species.

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Organizational Affiliation: 
• †Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States.
‡Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, United States.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 225.84 kDa 
• Atom Count: 15,675 
• Modeled Residue Count: 2,035 
• Deposited Residue Count: 2,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-aminoadipic semialdehyde dehydrogenase	A, B, C, D	513	Homo sapiens	Mutation(s): 0  Gene Names: ALDH7A1, ATQ1 EC: 1.2.1.31 (PDB Primary Data), 1.2.1.3 (PDB Primary Data), 1.2.1.8 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49419 (Homo sapiens) Explore P49419  Go to UniProtKB:  P49419
PHAROS:  P49419 GTEx:  ENSG00000164904

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], G [auth B], I [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
3W9	F [auth A], H [auth B], J [auth C], L [auth D]	4-(diethylamino)benzaldehyde C11 H15 N O MNFZZNNFORDXSV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.235 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.263	α = 90
b = 160.263	β = 90
c = 320.482	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Luo, M., Tanner, J.J.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary