Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 1285 
• Modelled Residue Count: 123 
• Deposited Residue Count: 123 
• Unique protein chains: 1

4O0A

Fragment-Based Discovery of a Potent Inhibitor of Replication Protein A Protein-Protein Interactions

• PDB DOI: 10.2210/pdb4O0A/pdb

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


• Deposited: 2013-12-13 Released: 2014-01-08 
• Deposition Author(s): Feldkamp, M.D., Frank, A.O., Kennedy, J.P., Waterson, A.G., Olejniczak, E.T., Pelz, N.F., Patrone, J.D., Vangamudi, B., Camper, D.V., Rossanese, O.W., Fesik, S.W., Chazin, W.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.176 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 

Literature

Discovery of a potent inhibitor of replication protein a protein-protein interactions using a fragment-linking approach.

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

(2013) J Med Chem 56: 9242-9250

• PubMed: 24147804 
• DOI: 10.1021/jm401333u
• Primary Citation of Related Structures:  
  4LUO, 4LUV, 4LUZ, 4LW1, 4LWC, 4O0A


• PubMed Abstract: 
  

Replication protein A (RPA), the major eukaryotic single-stranded DNA (ssDNA)-binding protein, is involved in nearly all cellular DNA transactions. The RPA N-terminal domain (RPA70N) is a recruitment site for proteins involved in DNA-damage response and repair. Selective inhibition of these protein-protein interactions has the potential to inhibit the DNA-damage response and to sensitize cancer cells to DNA-damaging agents without affecting other functions of RPA. To discover a potent, selective inhibitor of the RPA70N protein-protein interactions to test this hypothesis, we used NMR spectroscopy to identify fragment hits that bind to two adjacent sites in the basic cleft of RPA70N. High-resolution X-ray crystal structures of RPA70N-ligand complexes revealed how these fragments bind to RPA and guided the design of linked compounds that simultaneously occupy both sites. We have synthesized linked molecules that bind to RPA70N with submicromolar affinity and minimal disruption of RPA's interaction with ssDNA.

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Organizational Affiliation: 

Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States.

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2P9	B [auth A]	5-{4-[({[4-(5-carboxyfuran-2-yl)-2-chlorophenyl]carbonothioyl}amino)methyl]phenyl}-1-(3,4-dichlorophenyl)-1H-pyrazole-3-carboxylic acid C29 H18 Cl3 N3 O5 S RSWLTGWUCSWTHA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2P9	BindingDB:  4O0A	Kd: min: 190, max: 5200 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.176 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.912	α = 90
b = 53.582	β = 90
c = 53.932	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

• Deposited Date: 2013-12-13 
• Released Date: 2014-01-08 
Deposition Author(s): Feldkamp, M.D., Frank, A.O., Kennedy, J.P., Waterson, A.G., Olejniczak, E.T., Pelz, N.F., Patrone, J.D., Vangamudi, B., Camper, D.V., Rossanese, O.W., Fesik, S.W., Chazin, W.J.

Revision History  

• Version 1.0: 2014-01-08
  Type: Initial release
  
• Version 1.1: 2014-11-05
  Changes: Structure summary
• Version 1.2: 2018-10-10
  Changes: Data collection, Database references, Structure summary