2RD6 | pdb_00002rd6

PARP complexed with A861695

• PDB DOI: https://doi.org/10.2210/pdb2RD6/pdb

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


• Deposited: 2007-09-21 Released: 2008-09-23 
• Deposition Author(s): Park, C.H.

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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

Literature

PARP complexed with A861695

Park, C.H.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 1	A	350	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
78P	B [auth A]	(2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium C13 H16 N4 O JNAHVYVRKWKWKQ-CYBMUJFWSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 94.537	α = 90
b = 94.537	β = 90
c = 68.502	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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