4OQA

Structure of Human PARP-1 bound to a DNA double strand break in complex with (2Z)-2-(2,4-dihydroxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.298 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Discovery and Structure-Activity Relationship of Novel 2,3-Dihydrobenzofuran-7-carboxamide and 2,3-Dihydrobenzofuran-3(2H)-one-7-carboxamide Derivatives as Poly(ADP-ribose)polymerase-1 Inhibitors.

Patel, M.R.Bhatt, A.Steffen, J.D.Chergui, A.Murai, J.Pommier, Y.Pascal, J.M.Trombetta, L.D.Fronczek, F.R.Talele, T.T.

(2014) J.Med.Chem. 57: 5579-5601

  • DOI: 10.1021/jm5002502
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Novel substituted 2,3-dihydrobenzofuran-7-carboxamide (DHBF-7-carboxamide) and 2,3-dihydrobenzofuran-3(2H)-one-7-carboxamide (DHBF-3-one-7-carboxamide) derivatives were synthesized and evaluated as inhibitors of poly(ADP-ribose)polymerase-1 (PARP-1). ...

    Novel substituted 2,3-dihydrobenzofuran-7-carboxamide (DHBF-7-carboxamide) and 2,3-dihydrobenzofuran-3(2H)-one-7-carboxamide (DHBF-3-one-7-carboxamide) derivatives were synthesized and evaluated as inhibitors of poly(ADP-ribose)polymerase-1 (PARP-1). A structure-based design strategy resulted in lead compound 3 (DHBF-7-carboxamide; IC50 = 9.45 μM). To facilitate synthetically feasible derivatives, an alternative core was designed, DHBF-3-one-7-carboxamide (36, IC50 = 16.2 μM). The electrophilic 2-position of this scaffold was accessible for extended modifications. Substituted benzylidene derivatives at the 2-position were found to be the most potent, with 3',4'-dihydroxybenzylidene 58 (IC50 = 0.531 μM) showing a 30-fold improvement in potency. Various heterocycles attached at the 4'-hydroxyl/4'-amino of the benzylidene moiety resulted in significant improvement in inhibition of PARP-1 activity (e.g., compounds 66-68, 70, 72, and 73; IC50 values from 0.718 to 0.079 μM). Compound 66 showed selective cytotoxicity in BRCA2-deficient DT40 cells. Crystal structures of three inhibitors (compounds (-)-13c, 59, and 65) bound to a multidomain PARP-1 structure were obtained, providing insights into further development of these inhibitors.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University , Queens, New York 11439, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly [ADP-ribose] polymerase 1
A, D
267Homo sapiensMutation(s): 0 
Gene Names: PARP1 (ADPRT, PPOL)
EC: 2.4.2.30
Find proteins for P09874 (Homo sapiens)
Go to Gene View: PARP1
Go to UniProtKB:  P09874
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Poly [ADP-ribose] polymerase 1
C, F
505Homo sapiensMutation(s): 0 
Gene Names: PARP1 (ADPRT, PPOL)
EC: 2.4.2.30
Find proteins for P09874 (Homo sapiens)
Go to Gene View: PARP1
Go to UniProtKB:  P09874
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (26-MER)M,N26N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
2US
Query on 2US

Download SDF File 
Download CCD File 
C
(2Z)-2-(2,4-dihydroxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide
C16 H11 N O5
IANCBPDHSPOPRZ-MLPAPPSSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2USIC50: 753 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.298 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.160α = 90.00
b = 114.230β = 90.00
c = 294.240γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
REFMACrefinement
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2014-07-09
    Type: Database references
  • Version 1.2: 2014-07-23
    Type: Database references
  • Version 1.3: 2017-07-26
    Type: Source and taxonomy
  • Version 1.4: 2018-01-24
    Type: Structure summary