4R4C | pdb_00004r4c

Structure of RPA70N in complex with 5-(4-((4-(5-carboxyfuran-2-yl)-2-chlorobenzamido)methyl)phenyl)-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb4R4C/pdb

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


• 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: 1.40 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1021/ml5003629
• Primary Citation Related Structures: 
  4R4C, 4R4I, 4R4O, 4R4Q, 4R4T


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 14.11 kDa 
• Atom Count: 1,175 
• Modeled Residue Count: 123 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 70 kDa DNA-binding subunit	A	123	Homo sapiens	Mutation(s): 1  Gene Names: RPA1, REPA1, RPA70
UniProt & NIH Common Fund Data Resources
Find proteins for P27694 (Homo sapiens) Explore P27694  Go to UniProtKB:  P27694
PHAROS:  P27694 GTEx:  ENSG00000132383

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3HS	B [auth A]	5-[4-({[4-(5-carboxyfuran-2-yl)-2-chlorobenzoyl]amino}methyl)phenyl]-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid C29 H18 Cl3 N3 O6 KMDVWGXHTUXJOW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.07	α = 90
b = 53.864	β = 90
c = 53.977	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description