6VKO | pdb_00006vko

Crystal Structure of human PARP-1 CAT domain bound to inhibitor UKTT15

• PDB DOI: https://doi.org/10.2210/pdb6VKO/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-01-21 Released: 2020-06-17 
• Deposition Author(s): Langelier, M.F., Pascal, J.M.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.312 (Depositor), 0.318 (DCC) 
• R-Value Work: 
  0.284 (Depositor), 0.290 (DCC) 
• R-Value Observed: 
  0.286 (Depositor) 

Starting Model: experimental

Literature

Structural basis for allosteric PARP-1 retention on DNA breaks.

Zandarashvili, L., Langelier, M.F., Velagapudi, U.K., Hancock, M.A., Steffen, J.D., Billur, R., Hannan, Z.M., Wicks, A.J., Krastev, D.B., Pettitt, S.J., Lord, C.J., Talele, T.T., Pascal, J.M., Black, B.E.

(2020) Science 368

• PubMed: 32241924 
• DOI: https://doi.org/10.1126/science.aax6367
• Primary Citation Related Structures: 
  6NTU, 6VKK, 6VKO, 6VKQ


• PubMed Abstract: 
  

  The success of poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors (PARPi) to treat cancer relates to their ability to trap PARP-1 at the site of a DNA break. Although different forms of PARPi all target the catalytic center of the enzyme, they have variable abilities to trap PARP-1. We found that several structurally distinct PARPi drive PARP-1 allostery to promote release from a DNA break. Other inhibitors drive allostery to retain PARP-1 on a DNA break. Further, we generated a new PARPi compound, converting an allosteric pro-release compound to a pro-retention compound and increasing its ability to kill cancer cells. These developments are pertinent to clinical applications where PARP-1 trapping is either desirable or undesirable.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Département de Biochimie and Médecine Moléculaire, Faculté de Médecine, Université de Montréal, Montréal, QC H3C 3J7, Canada.
Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA.
SPR-MS Facility, McGill University, Montréal, Quebec, Canada.
Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London SW3 6JB, UK.
Département de Biochimie and Médecine Moléculaire, Faculté de Médecine, Université de Montréal, Montréal, QC H3C 3J7, Canada. [e-mail] [e-mail].
Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 169.38 kDa 
• Atom Count: 10,970 
• Modeled Residue Count: 1,360 
• Deposited Residue Count: 1,488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 1	A, B, C, D	372	Homo sapiens	Mutation(s): 1  Gene Names: PARP1, ADPRT, PPOL EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens) Explore P09874  Go to UniProtKB:  P09874
PHAROS:  P09874 GTEx:  ENSG00000143799

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L1S (Subject of Investigation/LOI)	E [auth A], I [auth B], M [auth C], Q [auth D]	methyl 2-{4-[4-(7-carbamoyl-1H-benzimidazol-2-yl)benzene-1-carbonyl]piperazin-1-yl}pyrimidine-5-carboxylate C25 H23 N7 O4 ASPUHGRKEUIGTD-UHFFFAOYSA-N
SO4	F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C], R [auth D], S [auth D], T [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.312 (Depositor), 0.318 (DCC) 
• R-Value Work:  0.284 (Depositor), 0.290 (DCC) 
• R-Value Observed: 0.286 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.701	α = 90
b = 129.751	β = 111.36
c = 102.72	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Langelier, M.F., Pascal, J.M.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	BMA342854

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary