6WS5

Rational drug design of phenazopyridine derivatives as novel inhibitors of Rev1-CT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Drug Design of Phenazopyridine Derivatives as Inhibitors of Rev1 Interactions in Translesion Synthesis.

McPherson, K.S.Zaino, A.M.Dash, R.C.Rizzo, A.A.Li, Y.Hao, B.Bezsonova, I.Hadden, M.K.Korzhnev, D.M.

(2021) ChemMedChem 16: 1126-1132

  • DOI: https://doi.org/10.1002/cmdc.202000893
  • Primary Citation of Related Structures:  
    6WS0, 6WS5

  • PubMed Abstract: 

    Rev1 is a protein scaffold of the translesion synthesis (TLS) pathway, which employs low-fidelity DNA polymerases for replication of damaged DNA. The TLS pathway helps cancers tolerate DNA damage induced by genotoxic chemotherapy, and increases mutagenesis in tumors, thus accelerating the onset of chemoresistance. TLS inhibitors have emerged as potential adjuvant drugs to enhance the efficacy of first-line chemotherapy, with the majority of reported inhibitors targeting protein-protein interactions (PPIs) of the Rev1 C-terminal domain (Rev1-CT). We previously identified phenazopyridine (PAP) as a scaffold to disrupt Rev1-CT PPIs with Rev1-interacting regions (RIRs) of TLS polymerases. To explore the structure-activity relationships for this scaffold, we developed a protocol for co-crystallization of compounds that target the RIR binding site on Rev1-CT with a triple Rev1-CT/Rev7 R124A /Rev3-RBM1 complex, and solved an X-ray crystal structure of Rev1-CT bound to the most potent PAP analogue. The structure revealed an unexpected binding pose of the compound and informed changes to the scaffold to improve its affinity for Rev1-CT. We synthesized eight additional PAP derivatives, with modifications to the scaffold driven by the structure, and evaluated their binding to Rev1-CT by microscale thermophoresis (MST). Several second-generation PAP derivatives showed an affinity for Rev1-CT that was improved by over an order of magnitude, thereby validating the structure-based assumptions that went into the compound design.


  • Organizational Affiliation

    Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein REV1A [auth HHH]95Homo sapiensMutation(s): 0 
Gene Names: REV1REV1L
EC: 2.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBZ9 (Homo sapiens)
Explore Q9UBZ9 
Go to UniProtKB:  Q9UBZ9
PHAROS:  Q9UBZ9
GTEx:  ENSG00000135945 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBZ9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitotic spindle assembly checkpoint protein MAD2BB [auth CCC]227Homo sapiensMutation(s): 1 
Gene Names: MAD2L2MAD2BREV7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI95 (Homo sapiens)
Explore Q9UI95 
Go to UniProtKB:  Q9UI95
PHAROS:  Q9UI95
GTEx:  ENSG00000116670 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UI95
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase zeta catalytic subunitC [auth ZZZ]52Homo sapiensMutation(s): 0 
Gene Names: REV3LPOLZREV3
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for O60673 (Homo sapiens)
Explore O60673 
Go to UniProtKB:  O60673
PHAROS:  O60673
GTEx:  ENSG00000009413 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60673
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U8M (Subject of Investigation/LOI)
Query on U8M

Download Ideal Coordinates CCD File 
D [auth HHH]3-[(Z)-(2,3-difluorophenyl)diazenyl]pyridine-2,6-diamine
C11 H9 F2 N5
KBEPGXDKUHLALK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.019α = 90
b = 73.023β = 90
c = 85.554γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA233959

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description