Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 14102.17 
• Atom Count: 1005 
• Residue Count: 123 
• Unique protein chains: 1

4R4Q

Crystal structure of RPA70N in complex with 5-(3-((N-(4-(5-carboxyfuran-2-yl)benzyl)acetamido)methyl)phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid

• DOI: 10.2210/pdb4R4Q/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2014-08-19 Released: 2014-11-19 
• Deposition Author(s): Feldkamp, M.D., Waterson, A.G., Kennedy, J.P., Patrone, J.D., Pelz, N.F., Frank, A.O., Vangamudi, B., Sousa-Fagundes, E.M., Rossanese, O.W., Fesik, S.W., Chazin, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.188 
• R-Value Work: 0.148 

Literature

Diphenylpyrazoles as replication protein a inhibitors.

Waterson, A.G., Kennedy, J.P., Patrone, J.D., Pelz, N.F., Feldkamp, M.D., Frank, A.O., Vangamudi, B., Souza-Fagundes, E.M., Rossanese, O.W., Chazin, W.J., Fesik, S.W.

(2015) ACS Med Chem Lett 6: 140-145

• PubMed: 25699140 
• DOI: 10.1021/ml5003629
• Primary Citation of Related Structures:  
  4R4T, 4R4O, 4R4I, 4R4C


• PubMed Abstract: 
  

Replication Protein A is the primary eukaryotic ssDNA binding protein that has a central role in initiating the cellular response to DNA damage. RPA recruits multiple proteins to sites of DNA damage via the N-terminal domain of the 70 kDa subunit (RPA70N). Here we describe the optimization of a diphenylpyrazole carboxylic acid series of inhibitors of these RPA-protein interactions. We evaluated substituents on the aromatic rings as well as the type and geometry of the linkers used to combine fragments, ultimately leading to submicromolar inhibitors of RPA70N protein-protein interactions.

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Organizational Affiliation: 

Department of Biochemistry, Department of Pharmacology, Vanderbilt University School of Medicine, and Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37232, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Replication protein A 70 kDa DNA-binding subunit	A	123	Homo sapiens	Mutation(s): 1  Gene Names: RPA1 (REPA1, RPA70)
Find proteins for P27694 (Homo sapiens) Go to Gene View: RPA1 Go to UniProtKB:  P27694

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
3HZ	A	5-[4-({acetyl[4-(5-carboxyfuran-2-yl)benzyl]amino}methyl)phenyl]-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid C31 H23 Cl2 N3 O6 BZWATIDSWCBFFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.188 
• R-Value Work: 0.148 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 38.161	α = 90.00
b = 53.934	β = 90.00
c = 53.975	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PHENIX	phasing
PHENIX	model building
HKL-2000	data collection
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-19 
• Released Date: 2014-11-19 
• Deposition Author(s): Feldkamp, M.D., Waterson, A.G., Kennedy, J.P., Patrone, J.D., Pelz, N.F., Frank, A.O., Vangamudi, B., Sousa-Fagundes, E.M., Rossanese, O.W., Fesik, S.W., Chazin, W.J.

Revision History 

• Version 1.0: 2014-11-19
  Type: Initial release
• Version 1.1: 2015-03-11
  Type: Database references