6V3W

Human Poly(ADP-Ribose) Polymerase 12, Catalytic fragment with four point mutations in complex with RBN-2397


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.5 of the entry. See complete history


Literature

PARP7 negatively regulates the type I interferon response in cancer cells and its inhibition triggers antitumor immunity.

Gozgit, J.M.Vasbinder, M.M.Abo, R.P.Kunii, K.Kuplast-Barr, K.G.Gui, B.Lu, A.Z.Molina, J.R.Minissale, E.Swinger, K.K.Wigle, T.J.Blackwell, D.J.Majer, C.R.Ren, Y.Niepel, M.Varsamis, Z.A.Nayak, S.P.Bamberg, E.Mo, J.R.Church, W.D.Mady, A.S.A.Song, J.Utley, L.Rao, P.E.Mitchison, T.J.Kuntz, K.W.Richon, V.M.Keilhack, H.

(2021) Cancer Cell 39: 1214-1226.e10

  • DOI: https://doi.org/10.1016/j.ccell.2021.06.018
  • Primary Citation of Related Structures:  
    6V3W

  • PubMed Abstract: 

    PARP7 is a monoPARP that catalyzes the transfer of single units of ADP-ribose onto substrates to change their function. Here, we identify PARP7 as a negative regulator of nucleic acid sensing in tumor cells. Inhibition of PARP7 restores type I interferon (IFN) signaling responses to nucleic acids in tumor models. Restored signaling can directly inhibit cell proliferation and activate the immune system, both of which contribute to tumor regression. Oral dosing of the PARP7 small-molecule inhibitor, RBN-2397, results in complete tumor regression in a lung cancer xenograft and induces tumor-specific adaptive immune memory in an immunocompetent mouse cancer model, dependent on inducing type I IFN signaling in tumor cells. PARP7 is a therapeutic target whose inhibition induces both cancer cell-autonomous and immune stimulatory effects via enhanced IFN signaling. These data support the targeting of a monoPARP in cancer and introduce a potent and selective PARP7 inhibitor to enter clinical development.


  • Organizational Affiliation

    Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA. Electronic address: jgozgit@ribontx.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein mono-ADP-ribosyltransferase PARP12198Homo sapiensMutation(s): 4 
Gene Names: PARP12ZC3HDC1
EC: 2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0J9 (Homo sapiens)
Explore Q9H0J9 
Go to UniProtKB:  Q9H0J9
PHAROS:  Q9H0J9
GTEx:  ENSG00000059378 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H0J9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QO4 (Subject of Investigation/LOI)
Query on QO4

Download Ideal Coordinates CCD File 
B [auth A]5-{[(2S)-1-(3-oxo-3-{4-[5-(trifluoromethyl)pyrimidin-2-yl]piperazin-1-yl}propoxy)propan-2-yl]amino}-4-(trifluoromethyl)pyridazin-3(2H)-one
C20 H23 F6 N7 O3
UQZCQKXJAXKZQH-LBPRGKRZSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
QO4 BindingDB:  6V3W IC50: 5.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.466α = 90
b = 80.466β = 90
c = 142.648γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references
  • Version 1.2: 2021-08-25
    Changes: Database references
  • Version 1.3: 2021-09-29
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary