2RD6 | pdb_00002rd6

PARP complexed with A861695

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.308 (Depositor) 
  • R-Value Work: 
    0.228 (Depositor) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2RD6

This is version 1.2 of the entry. See complete history. 

Literature

PARP complexed with A861695

Park, C.H.

To be published.

Macromolecule Content 

  • Total Structure Weight: 39.41 kDa 
  • Atom Count: 2,939 
  • Modeled Residue Count: 350 
  • Deposited Residue Count: 350 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1350Homo sapiensMutation(s): 0 
Gene Names: PARP1, ADPRT, PPOL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
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
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
78P

Query on 78P


Download:Ideal Coordinates CCD File
B [auth A](2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium
C13 H16 N4 O
JNAHVYVRKWKWKQ-CYBMUJFWSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
78P BindingDB:  2RD6 Ki: 5 (nM) from 1 assay(s)
Kd: 1.7 (nM) from 1 assay(s)
IC50: min: 1, max: 355 (nM) from 16 assay(s)
EC50: min: 2, max: 3000 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.308 (Depositor) 
  • R-Value Work:  0.228 (Depositor) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.537α = 90
b = 94.537β = 90
c = 68.502γ = 120
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Released Date: 2008-09-23 
    • Deposition Author(s): Park, C.H.

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary