Co-crystal structure of caPCNA bound to AOH1160 derivative 1LE

Experimental Data Snapshot

  • Resolution: 2.81 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Small molecule targeting of transcription-replication conflict for selective chemotherapy.

Gu, L.Li, M.Li, C.M.Haratipour, P.Lingeman, R.Jossart, J.Gutova, M.Flores, L.Hyde, C.Kenjic, N.Li, H.Chung, V.Li, H.Lomenick, B.Von Hoff, D.D.Synold, T.W.Aboody, K.S.Liu, Y.Horne, D.Hickey, R.J.Perry, J.J.P.Malkas, L.H.

(2023) Cell Chem Biol 30: 1235

  • DOI: https://doi.org/10.1016/j.chembiol.2023.07.001
  • Primary Citation of Related Structures:  
    8GL9, 8GLA

  • PubMed Abstract: 

    Targeting transcription replication conflicts, a major source of endogenous DNA double-stranded breaks and genomic instability could have important anticancer therapeutic implications. Proliferating cell nuclear antigen (PCNA) is critical to DNA replication and repair processes. Through a rational drug design approach, we identified a small molecule PCNA inhibitor, AOH1996, which selectively kills cancer cells. AOH1996 enhances the interaction between PCNA and the largest subunit of RNA polymerase II, RPB1, and dissociates PCNA from actively transcribed chromatin regions, while inducing DNA double-stranded breaks in a transcription-dependent manner. Attenuation of RPB1 interaction with PCNA, by a point mutation in RPB1's PCNA-binding region, confers resistance to AOH1996. Orally administrable and metabolically stable, AOH1996 suppresses tumor growth as a monotherapy or as a combination treatment but causes no discernable side effects. Inhibitors of transcription replication conflict resolution may provide a new and unique therapeutic avenue for exploiting this cancer-selective vulnerability.

  • Organizational Affiliation

    Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA. Electronic address: Lgu@coh.org.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen
A, B, C, D
261Homo sapiensMutation(s): 0 
Gene Names: PCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens)
Explore P12004 
Go to UniProtKB:  P12004
PHAROS:  P12004
GTEx:  ENSG00000132646 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12004
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZQW

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
L [auth B]
M [auth B]
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B]
C28 H24 N2 O5
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth B]
K [auth B]
O [auth C]
E [auth A],
F [auth A],
J [auth B],
K [auth B],
O [auth C],
P [auth C],
Q [auth D],
R [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.81 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.145α = 90
b = 197.145β = 90
c = 126.979γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesW81XWH1910327

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Author supporting evidence, Database references, Structure summary
  • Version 1.2: 2023-08-09
    Changes: Database references
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.4: 2023-11-01
    Changes: Database references