5NQE | pdb_00005nqe

Human PARP14 (ARTD8), catalytic fragment in complex with an N-aryl piperazine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5NQE/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-20 Released: 2017-05-24 
• Deposition Author(s): Karlberg, T., Thorsell, A.G., Schuler, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.258 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Design and synthesis of potent inhibitors of the mono(ADP-ribosyl)transferase, PARP14.

Upton, K., Meyers, M., Thorsell, A.G., Karlberg, T., Holechek, J., Lease, R., Schey, G., Wolf, E., Lucente, A., Schuler, H., Ferraris, D.

(2017) Bioorg Med Chem Lett 27: 2907-2911

• PubMed: 28495083 
• DOI: https://doi.org/10.1016/j.bmcl.2017.04.089
• Primary Citation Related Structures: 
  5NQE


• PubMed Abstract: 
  

  A series of (Z)-4-(3-carbamoylphenylamino)-4-oxobut-2-enyl amides were synthesized and tested for their ability to inhibit the mono-(ADP-ribosyl)transferase, PARP14 (a.k.a. BAL-2; ARTD-8). Two synthetic routes were established for this series and several compounds were identified as sub-micromolar inhibitors of PARP14, the most potent of which was compound 4t, IC ₅₀ =160nM. Furthermore, profiling other members of this series identified compounds with >20-fold selectivity over PARP5a/TNKS1, and modest selectivity over PARP10, a closely related mono-(ADP-ribosyl)transferase.

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Organizational Affiliation: 
• McDaniel College, 2 College Hill, Westminster, MD 21157, United States.
Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Scheeles väg 2, S-17177 Stockholm, Sweden.
Stevenson University, 1525 Greenspring Valley Rd, Stevenson, MD 21153, United States.
McDaniel College, 2 College Hill, Westminster, MD 21157, United States. 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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.03 kDa 
• Atom Count: 3,005 
• Modeled Residue Count: 360 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 14	A, B	193	Homo sapiens	Mutation(s): 0  Gene Names: PARP14, BAL2, KIAA1268 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q460N5 (Homo sapiens) Explore Q460N5  Go to UniProtKB:  Q460N5
PHAROS:  Q460N5 GTEx:  ENSG00000173193

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
94Z	C [auth A], D [auth B]	3-[[4-[4-(4-fluorophenyl)piperazin-1-yl]-4-oxidanylidene-butanoyl]amino]benzamide C21 H23 F N4 O3 XOGWZMUISDMZAY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.258 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.43	α = 90
b = 90.36	β = 116.42
c = 80.07	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
xia2	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Karlberg, T., Thorsell, A.G., Schuler, H.

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary