4IJL

Fragment-based Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A

• PDB DOI: https://doi.org/10.2210/pdb4IJL/pdb

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


• Deposited: 2012-12-21 Released: 2013-08-14 
• Deposition Author(s): Feldkamp, M.D., Patrone, J.D., Kennedy, J.P., Frank, A.O., Vangamudi, B., Pelz, N.F., Rossanese, O.W., Waterson, A.G., Fesik, S.W., Chazin, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.233 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A.

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

(2013) ACS Med Chem Lett 4: 601-605

• PubMed: 23914285 
• DOI: https://doi.org/10.1021/ml400032y
• Primary Citation of Related Structures:  
  4IJH, 4IJL


• PubMed Abstract: 
  

  Replication Protein A (RPA) is a ssDNA binding protein that is essential for DNA replication and repair. The initiation of the DNA damage response by RPA is mediated by protein-protein interactions involving the N-terminal domain of the 70 kDa subunit with partner proteins. Inhibition of these interactions increases sensitivity towards DNA damage and replication stress and may therefore be a potential strategy for cancer drug discovery. Towards this end, we have discovered two lead series of compounds, derived from hits obtained from a fragment-based screen, that bind to RPA70N with low micromolar affinity and inhibit the binding of an ATRIP-derived peptide to RPA. These compounds may offer a promising starting point for the discovery of clinically useful RPA inhibitors.

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Organizational Affiliation: 

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232 (USA).

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: 14.3 kDa 
• Atom Count: 1,071 
• Modelled Residue Count: 122 
• 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: REPA1, RPA1, 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
1EK	B [auth A], C [auth A]	{[5-(3-chloro-1-benzothiophen-2-yl)-4-phenyl-4H-1,2,4-triazol-3-yl]sulfanyl}acetic acid C18 H12 Cl N3 O2 S2 GNEUDTMFXMASKC-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1EK	PDBBind:  4IJL	Kd: 1.35e+5 (nM) from 1 assay(s)
	BindingDB:  4IJL	Kd: 1.35e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.233 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.551	α = 90
b = 53.569	β = 90
c = 54.259	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: 2013-08-14 
Deposition Author(s): Feldkamp, M.D., Patrone, J.D., Kennedy, J.P., Frank, A.O., Vangamudi, B., Pelz, N.F., Rossanese, O.W., Waterson, A.G., Fesik, S.W., Chazin, W.J.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description