7UM9

Human ALDH1A1 with bound compound CM38


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Novel ALDH1A1 Inhibitor Blocks Platinum-Induced Senescence and Stemness in Ovarian Cancer.

Muralikrishnan, V.Fang, F.Given, T.C.Podicheti, R.Chtcherbinine, M.Metcalfe, T.X.Sriramkumar, S.O'Hagan, H.M.Hurley, T.D.Nephew, K.P.

(2022) Cancers (Basel) 14

  • DOI: https://doi.org/10.3390/cancers14143437
  • Primary Citation of Related Structures:  
    7UM9

  • PubMed Abstract: 

    Ovarian cancer is a deadly disease attributed to late-stage detection as well as recurrence and the development of chemoresistance. Ovarian cancer stem cells (OCSCs) are hypothesized to be largely responsible for the emergence of chemoresistant tumors. Although chemotherapy may initially succeed at decreasing the size and number of tumors, it leaves behind residual malignant OCSCs. In this study, we demonstrate that aldehyde dehydrogenase 1A1 (ALDH1A1) is essential for the survival of OCSCs. We identified a first-in-class ALDH1A1 inhibitor, compound 974 , and used 974 as a tool to decipher the mechanism of stemness regulation by ALDH1A1. The treatment of OCSCs with 974 significantly inhibited ALDH activity, the expression of stemness genes, and spheroid and colony formation. An in vivo limiting dilution assay demonstrated that 974 significantly inhibited CSC frequency. A transcriptomic sequencing of cells treated with 974 revealed a significant downregulation of genes related to stemness and chemoresistance as well as senescence and the senescence-associated secretory phenotype (SASP). We confirmed that 974 inhibited the senescence and stemness induced by platinum-based chemotherapy in functional assays. Overall, these data establish that ALDH1A1 is essential for OCSC survival and that ALDH1A1 inhibition suppresses chemotherapy-induced senescence and stemness. Targeting ALDH1A1 using small-molecule inhibitors in combination with chemotherapy therefore presents a promising strategy to prevent ovarian cancer recurrence and has the potential for clinical translation.


  • Organizational Affiliation

    Cell, Molecular and Cancer Biology Graduate Program, Medical Sciences Department, Indiana University School of Medicine, Bloomington, IN 47405, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinal dehydrogenase 1501Homo sapiensMutation(s): 0 
Gene Names: ALDH1A1ALDCALDH1PUMB1
EC: 1.2.1 (PDB Primary Data), 1.2.1.36 (PDB Primary Data), 1.2.1.19 (UniProt), 1.2.1.28 (UniProt), 1.2.1.3 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00352 (Homo sapiens)
Explore P00352 
Go to UniProtKB:  P00352
PHAROS:  P00352
GTEx:  ENSG00000165092 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00352
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
F [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
NQR (Subject of Investigation/LOI)
Query on NQR

Download Ideal Coordinates CCD File 
B [auth A](4-methylfuro[3,2-c]quinolin-2-yl)(piperidin-1-yl)methanone
C18 H18 N2 O2
CKBASHMUSIQRHS-UHFFFAOYSA-N
YB
Query on YB

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.108α = 90
b = 109.108β = 90
c = 83.077γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-04-26 
  • Deposition Author(s): Hurley, T.D.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA214567

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-11-08
    Changes: Database references