5AC2

human aldehyde dehydrogenase 1A1 with duocarmycin analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition by Cytotoxic Duocarmycin Analogues.

Koch, M.F.Harteis, S.Blank, I.D.Pestel, G.Tietze, L.F.Ochsenfeld, C.Schneider, S.Sieber, S.A.

(2015) Angew Chem Int Ed Engl 54: 13550

  • DOI: 10.1002/anie.201505749
  • Primary Citation of Related Structures:  
    5AC0, 5AC2, 5AC1, 5ABM

  • PubMed Abstract: 
  • Analogues of the natural product duocarmycin bearing an indole moiety were shown to bind aldehyde dehydrogenase 1A1 (ALDH1A1) in addition to DNA, while derivatives without the indole solely addressed the ALDH1A1 protein. The molecular mechanism of selective ALDH1A1 inhibition by duocarmycin analogues was unraveled through cocrystallization, mutational studies, and molecular dynamics simulations ...

    Analogues of the natural product duocarmycin bearing an indole moiety were shown to bind aldehyde dehydrogenase 1A1 (ALDH1A1) in addition to DNA, while derivatives without the indole solely addressed the ALDH1A1 protein. The molecular mechanism of selective ALDH1A1 inhibition by duocarmycin analogues was unraveled through cocrystallization, mutational studies, and molecular dynamics simulations. The structure of the complex shows the compound embedded in a hydrophobic pocket, where it is stabilized by several crucial π-stacking and van der Waals interactions. This binding mode positions the cyclopropyl electrophile for nucleophilic attack by the noncatalytic residue Cys302, thereby resulting in covalent attachment, steric occlusion of the active site, and inhibition of catalysis. The selectivity of duocarmycin analogues for ALDH1A1 is unique, since only minor alterations in the sequence of closely related protein isoforms restrict compound accessibility.


    Organizational Affiliation

    Center for Integrated Protein Science Munich CIPSMDepartment of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany). stephan.sieber@tum.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINAL DEHYDROGENASE 1A501Homo sapiensMutation(s): 0 
Gene Names: ALDH1A1ALDCALDH1PUMB1
EC: 1.2.1.36 (PDB Primary Data), 1.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00352 (Homo sapiens)
Explore P00352 
Go to UniProtKB:  P00352
PHAROS:  P00352
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TXE (Subject of Investigation/LOI)
Query on TXE

Download Ideal Coordinates CCD File 
D [auth A][[(2R,3S,4R,5R)-5-[(3R)-3-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-ph osphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate
C21 H31 N7 O14 P2
FDIVXUDDFSHSAE-MTKBYBFRSA-L
 Ligand Interaction
K9P (Subject of Investigation/LOI)
Query on K9P

Download Ideal Coordinates CCD File 
B [auth A]1-[(1S)-1-methyl-5-oxidanyl-1,2-dihydrobenzo[e]indol-3-yl]hexan-1-one
C19 H23 N O2
RUAITRBXVQXTLB-CYBMUJFWSA-N
 Ligand Interaction
YB
Query on YB

Download Ideal Coordinates CCD File 
C [auth A], E [auth A], F [auth A]YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.123α = 90
b = 109.123β = 90
c = 83.175γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-30
    Changes: Database references
  • Version 1.2: 2015-11-18
    Changes: Database references