Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in complex with NVP-LTM531

Experimental Data Snapshot

  • Resolution: 2.49 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


CPSF3-dependent pre-mRNA processing as a druggable node in AML and Ewing's sarcoma.

Ross, N.T.Lohmann, F.Carbonneau, S.Fazal, A.Weihofen, W.A.Gleim, S.Salcius, M.Sigoillot, F.Henault, M.Carl, S.H.Rodriguez-Molina, J.B.Miller, H.R.Brittain, S.M.Murphy, J.Zambrowski, M.Boynton, G.Wang, Y.Chen, A.Molind, G.J.Wilbertz, J.H.Artus-Revel, C.G.Jia, M.Akinjiyan, F.A.Turner, J.Knehr, J.Carbone, W.Schuierer, S.Reece-Hoyes, J.S.Xie, K.Saran, C.Williams, E.T.Roma, G.Spencer, M.Jenkins, J.George, E.L.Thomas, J.R.Michaud, G.Schirle, M.Tallarico, J.Passmore, L.A.Chao, J.A.Beckwith, R.E.J.

(2020) Nat Chem Biol 16: 50-59

  • DOI: https://doi.org/10.1038/s41589-019-0424-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The post-genomic era has seen many advances in our understanding of cancer pathways, yet resistance and tumor heterogeneity necessitate multiple approaches to target even monogenic tumors. Here, we combine phenotypic screening with chemical genetics to identify pre-messenger RNA endonuclease cleavage and polyadenylation specificity factor 3 (CPSF3) as the target of JTE-607, a small molecule with previously unknown target. We show that CPSF3 represents a synthetic lethal node in a subset of acute myeloid leukemia (AML) and Ewing's sarcoma cancer cell lines. Inhibition of CPSF3 by JTE-607 alters expression of known downstream effectors in AML and Ewing's sarcoma lines, upregulates apoptosis and causes tumor-selective stasis in mouse xenografts. Mechanistically, it prevents the release of newly synthesized pre-mRNAs, resulting in read-through transcription and the formation of DNA-RNA hybrid R-loop structures. This study implicates pre-mRNA processing, and specifically CPSF3, as a druggable target providing an avenue to therapeutic intervention in cancer.

  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Cambridge, MA, USA. rohan.beckwith@novartis.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 3
A, B
478Homo sapiensMutation(s): 0 
Gene Names: CPSF3CPSF73
EC: 3.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKF6 (Homo sapiens)
Explore Q9UKF6 
Go to UniProtKB:  Q9UKF6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKF6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JBG (Subject of Investigation/LOI)
Query on JBG

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
C23 H27 Cl2 N3 O5
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
K [auth B]
O4 P
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.49 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.222α = 90
b = 106.222β = 90
c = 206.035γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description