6YAA

Structure of the (SR) Ca2+-ATPase bound to the inhibitor compound CAD204520 and TNP-ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Blockade of Oncogenic NOTCH1 with the SERCA Inhibitor CAD204520 in T Cell Acute Lymphoblastic Leukemia.

Marchesini, M.Gherli, A.Montanaro, A.Patrizi, L.Sorrentino, C.Pagliaro, L.Rompietti, C.Kitara, S.Heit, S.Olesen, C.E.Moller, J.V.Savi, M.Bocchi, L.Vilella, R.Rizzi, F.Baglione, M.Rastelli, G.Loiacono, C.La Starza, R.Mecucci, C.Stegmaier, K.Aversa, F.Stilli, D.Lund Winther, A.M.Sportoletti, P.Bublitz, M.Dalby-Brown, W.Roti, G.

(2020) Cell Chem Biol 27: 678

  • DOI: https://doi.org/10.1016/j.chembiol.2020.04.002
  • Primary Citation of Related Structures:  
    6YAA

  • PubMed Abstract: 

    The identification of SERCA (sarco/endoplasmic reticulum calcium ATPase) as a target for modulating gain-of-function NOTCH1 mutations in Notch-dependent cancers has spurred the development of this compound class for cancer therapeutics. Despite the innate toxicity challenge associated with SERCA inhibition, we identified CAD204520, a small molecule with better drug-like properties and reduced off-target Ca 2+ toxicity compared with the SERCA inhibitor thapsigargin. In this work, we describe the properties and complex structure of CAD204520 and show that CAD204520 preferentially targets mutated over wild-type NOTCH1 proteins in T cell acute lymphoblastic leukemia (T-ALL) and mantle cell lymphoma (MCL). Uniquely among SERCA inhibitors, CAD204520 suppresses NOTCH1-mutated leukemic cells in a T-ALL xenografted model without causing cardiac toxicity. This study supports the development of SERCA inhibitors for Notch-dependent cancers and extends their application to cases with isolated mutations in the PEST degradation domain of NOTCH1, such as MCL or chronic lymphocytic leukemia (CLL).


  • Organizational Affiliation

    University of Parma, Department of Medicine and Surgery, Parma 43126, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1994Oryctolagus cuniculusMutation(s): 0 
EC: 7.2.2.10
Membrane Entity: Yes 
UniProt
Find proteins for P04191 (Oryctolagus cuniculus)
Explore P04191 
Go to UniProtKB:  P04191
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04191
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
128
Query on 128

Download Ideal Coordinates CCD File 
B [auth A]SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE
C16 H17 N8 O19 P3
XFMMHXLUHKBKQE-UHEGPQQHSA-N
OHW (Subject of Investigation/LOI)
Query on OHW

Download Ideal Coordinates CCD File 
C [auth A]4-[2-[(2~{R})-2-[3-propyl-6-(trifluoromethyloxy)-1~{H}-indol-2-yl]piperidin-1-yl]ethyl]morpholine
C23 H32 F3 N3 O2
UNPIVXUWRQMOQC-OAQYLSRUSA-N
K
Query on K

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.632α = 90
b = 71.632β = 90
c = 588.306γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary