7LUN | pdb_00007lun

Human PARP14 (ARTD8), catalytic fragment in complex with RBN011980


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 
    0.278 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Targeted Degradation of PARP14 Using a Heterobifunctional Small Molecule.

Wigle, T.J.Ren, Y.Molina, J.R.Blackwell, D.J.Schenkel, L.B.Swinger, K.K.Kuplast-Barr, K.Majer, C.R.Church, W.D.Lu, A.Z.Mo, J.Abo, R.Cheung, A.Dorsey, B.W.Niepel, M.Perl, N.R.Vasbinder, M.M.Keilhack, H.Kuntz, K.W.

(2021) Chembiochem 22: 2107-2110

  • DOI: https://doi.org/10.1002/cbic.202100047
  • Primary Citation Related Structures: 
    7L9Y, 7LUN

  • PubMed Abstract: 

    PARP14 is an interferon-stimulated gene that is overexpressed in multiple tumor types, influencing pro-tumor macrophage polarization as well as suppressing the antitumor inflammation response by modulating IFN-γ and IL-4 signaling. PARP14 is a 203 kDa protein that possesses a catalytic domain responsible for the transfer of mono-ADP-ribose to its substrates. PARP14 also contains three macrodomains and a WWE domain which are binding modules for mono-ADP-ribose and poly-ADP-ribose, respectively, in addition to two RNA recognition motifs. Catalytic inhibitors of PARP14 have been shown to reverse IL-4 driven pro-tumor gene expression in macrophages, however it is not clear what roles the non-enzymatic biomolecular recognition motifs play in PARP14-driven immunology and inflammation. To further understand this, we have discovered a heterobifunctional small molecule designed based on a catalytic inhibitor of PARP14 that binds in the enzyme's NAD + -binding site and recruits cereblon to ubiquitinate it and selectively target it for degradation.


  • Organizational Affiliation
    • Ribon Therapeutics, 35 Cambridgepark Dr., Suite 300, Cambridge, MA 02140, USA.

Macromolecule Content 

  • Total Structure Weight: 180.73 kDa 
  • Atom Count: 12,718 
  • Modeled Residue Count: 1,488 
  • Deposited Residue Count: 1,552 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein mono-ADP-ribosyltransferase PARP14
A, B, C, D, E
A, B, C, D, E, F, G, H
194Homo sapiensMutation(s): 0 
Gene Names: PARP14BAL2KIAA1268
EC: 2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q460N5 (Homo sapiens)
Explore Q460N5 
Go to UniProtKB:  Q460N5
PHAROS:  Q460N5
GTEx:  ENSG00000173193 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ460N5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YFG
(Subject of Investigation/LOI)

Query on YFG



Download:Ideal Coordinates CCD File
I [auth A]
J [auth B]
K [auth C]
L [auth D]
M [auth E]
I [auth A],
J [auth B],
K [auth C],
L [auth D],
M [auth E],
O [auth F],
Q [auth G],
R [auth H]
7-(cyclopentylamino)-5-fluoro-2-{[(trans-4-hydroxycyclohexyl)sulfanyl]methyl}quinazolin-4(3H)-one
C20 H26 F N3 O2 S
FUHIIFURQIAPDZ-SHTZXODSSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
P [auth F],
S [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
N [auth E]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
YFG BindingDB:  7LUN IC50: min: 1000, max: 1000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free:  0.278 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.99α = 90
b = 153.66β = 108.7
c = 87.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary