6YAA | pdb_00006yaa

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

• PDB DOI: https://doi.org/10.2210/pdb6YAA/pdb

• Classification: HYDROLASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-03-11 Released: 2020-05-20 
• Deposition Author(s): Heit, S., Marchesini, M., Gherli, A., Montanaro, A., Patrizi, L., Sorrentino, C., Pagliaro, L., Rompietti, C., Kitara, S., Olesen, C.E., Moller, J.V., Savi, M., Bocchi, L., Vilella, R., Rizzi, F., Baglione, M., Rastelli, G., Loiacona, C., La Starza, R., Mecucci, C., Stegmair, K., Aversa, F., Stilli, D., Lund Winther, A.M., Sportoletti, P., Dalby-Brown, W., Roti, G., Bublitz, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.255 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

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

• PubMed: 32386594 
• DOI: https://doi.org/10.1016/j.chembiol.2020.04.002
• Primary Citation 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).

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Organizational Affiliation: 
• University of Parma, Department of Medicine and Surgery, Parma 43126, Italy.
University of Perugia, Department of Medicine, Hematology and Clinical Immunology, Perugia 06123, Italy.
Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
University of Oxford, Department of Biochemistry, Oxford OX1 3QU, UK.
Aarhus University, Department of Biomedicine, 8000 Aarhus C, Denmark.
University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parma 43124, Italy.
University of Parma, Department of Medicine and Surgery, Parma 43126, Italy; INBB - Biostructures and Biosystems National Institute, Rome 00136, Italy.
Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; The Broad Institute, Cambridge, MA 02142, USA.
Cado Biotechnology IvS, Copenhagen, Denmark.
University of Parma, Department of Medicine and Surgery, Parma 43126, Italy. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 110.8 kDa 
• Atom Count: 7,749 
• Modeled Residue Count: 994 
• Deposited Residue Count: 994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	A	994	Oryctolagus cuniculus	Mutation(s): 0  EC: 7.2.2.10 Membrane Entity: Yes
UniProt
Find proteins for P04191 (Oryctolagus cuniculus) Explore P04191  Go to UniProtKB:  P04191

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
128	B [auth A]	SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE C16 H16 N8 O19 P3 LQZBDVDATBCNNN-UHEGPQQHSA-N
OHW (Subject of Investigation/LOI)	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	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 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.632	α = 90
b = 71.632	β = 90
c = 588.306	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-20 
Deposition Author(s): Heit, S., Marchesini, M., Gherli, A., Montanaro, A., Patrizi, L., Sorrentino, C., Pagliaro, L., Rompietti, C., Kitara, S., Olesen, C.E., Moller, J.V., Savi, M., Bocchi, L., Vilella, R., Rizzi, F., Baglione, M., Rastelli, G., Loiacona, C., La Starza, R., Mecucci, C., Stegmair, K., Aversa, F., Stilli, D., Lund Winther, A.M., Sportoletti, P., Dalby-Brown, W., Roti, G., Bublitz, M.

Revision History  

• 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
• Version 2.0: 2026-04-15
  Changes: Data collection, Non-polymer description, Structure summary