6G0W

Human PARP14 (ARTD8), catalytic fragment in complex with inhibitor MCD72

• PDB DOI: https://doi.org/10.2210/pdb6G0W/pdb

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


• Deposited: 2018-03-20 Released: 2018-05-23 
• Deposition Author(s): Karlberg, T., Thorsell, A.G., Holechek, J., Lease, R., Ferraris, D., Schuler, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.275 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

Literature

Design, synthesis and evaluation of potent and selective inhibitors of mono-(ADP-ribosyl)transferases PARP10 and PARP14.

Holechek, J., Lease, R., Thorsell, A.G., Karlberg, T., McCadden, C., Grant, R., Keen, A., Callahan, E., Schuler, H., Ferraris, D.

(2018) Bioorg Med Chem Lett 28: 2050-2054

• PubMed: 29748053 
• DOI: https://doi.org/10.1016/j.bmcl.2018.04.056
• Primary Citation of Related Structures:  
  6G0W


• PubMed Abstract: 
  

  A series of diaryl ethers were designed and synthesized to discern the structure activity relationships against the two closely related mono-(ADP-ribosyl)transferases PARP10 and PARP14. Structure activity studies identified 8b as a sub-micromolar inhibitor of PARP10 with ∼15-fold selectivity over PARP14. In addition, 8k and 8m were discovered to have sub-micromolar potency against PARP14 and demonstrated moderate selectivity over PARP10. A crystal structure of the complex of PARP14 and 8b shows binding of the compound in a novel hydrophobic pocket and explains both potency and selectivity over other PARP family members. In addition, 8b, 8k and 8m also demonstrate selectivity over PARP1. Together, this study identified novel, potent and metabolically stable derivatives to use as chemical probes for these biologically interesting therapeutic targets.

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Organizational Affiliation: 

McDaniel College, 2 College Hill, Westminster, MD 21157, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.07 kDa 
• Atom Count: 3,059 
• Modelled Residue Count: 367 
• 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
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
EGW	C [auth A], D [auth B]	4-[3-[4-(4-fluorophenyl)piperidin-1-yl]carbonylphenoxy]benzamide C25 H23 F N2 O3 GKQVMMKXPPAKMY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EGW	Binding MOAD:  6G0W	IC50: 5200 (nM) from 1 assay(s)
	BindingDB:  6G0W	IC50: min: 5200, max: 5248 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.275 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.314	α = 90
b = 83.314	β = 90
c = 255.495	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Karlberg, T., Thorsell, A.G., Holechek, J., Lease, R., Ferraris, D., Schuler, H.

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2018-05-30
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description