6XVW | pdb_00006xvw

Catalytic domain of human PARP-1 in complex with the inhibitor MC2050


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.265 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.231 (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 1.1 of the entry. See complete history

Literature

From PARP1 to TNKS2 Inhibition: A Structure-Based Approach.

Tomassi, S.Pfahler, J.Mautone, N.Rovere, A.Esposito, C.Passeri, D.Pellicciari, R.Novellino, E.Pannek, M.Steegborn, C.Paiardini, A.Mai, A.Rotili, D.

(2020) ACS Med Chem Lett 11: 862-868

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00654
  • Primary Citation Related Structures: 
    6XVW

  • PubMed Abstract: 

    Tankyrases (TNKSs) have recently gained great consideration as potential targets in Wnt/β-catenin pathway-dependent solid tumors. Previously, we reported the 2-mercaptoquinazolin-4-one MC2050 as a micromolar PARP1 inhibitor. Here we show how the resolution of the X-ray structure of PARP1 in complex with MC2050, combined with the computational investigation of the structural differences between TNKSs and PARP1/2 active sites, provided the rationale for a structure-based drug design campaign that with a limited synthetic effort led to the discovery of the bis-quinazolinone 5 as a picomolar and selective TNKS2 inhibitor, endowed with antiproliferative effects in a colorectal cancer cell line (DLD-1) where the Wnt pathway is constitutively activated.


  • Organizational Affiliation
    • Department of Pharmacy, University of Naples, "Federico II", 80131 Naples, Italy.

Macromolecule Content 

  • Total Structure Weight: 81.03 kDa 
  • Atom Count: 5,908 
  • Modeled Residue Count: 691 
  • Deposited Residue Count: 708 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1
A, B
354Homo sapiensMutation(s): 0 
Gene Names: PARP1ADPRTPPOL
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09874
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O3H
(Subject of Investigation/LOI)

Query on O3H



Download:Ideal Coordinates CCD File
M [auth A],
R [auth B]
2-[2-(4-pyridin-2-ylpiperazin-1-yl)ethylsulfanyl]-3~{H}-quinazolin-4-one
C19 H21 N5 O S
AFXJUCILCGBUNX-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI

Query on NI



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
N [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
N [auth B],
O [auth B]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
O3H BindingDB:  6XVW IC50: 9.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.265 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.172α = 90
b = 86.727β = 90
c = 127.635γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description