7R8R | pdb_00007r8r

Physachenolide C with Bromodomain (BRD3-BD1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8L6Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Physachenolide C is a Potent, Selective BET Inhibitor.

Zerio, C.J.Sivinski, J.Wijeratne, E.M.K.Xu, Y.M.Ngo, D.T.Ambrose, A.J.Villa-Celis, L.Ghadirian, N.Clarkson, M.W.Zhang, D.D.Horton, N.C.Gunatilaka, A.A.L.Fromme, R.Chapman, E.

(2023) J Med Chem 66: 913-933

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01770
  • Primary Citation of Related Structures:  
    7R8R, 7S3P

  • PubMed Abstract: 

    A pulldown using a biotinylated natural product of interest in the 17β-hydroxywithanolide (17-BHW) class, physachenolide C (PCC), identified the bromodomain and extra-terminal domain (BET) family of proteins (BRD2, BRD3, and BRD4), readers of acetyl-lysine modifications and regulators of gene transcription, as potential cellular targets. BROMOscan bromodomain profiling and biochemical assays support PCC as a BET inhibitor with increased selectivity for bromodomain (BD)-1 of BRD3 and BRD4, and X-ray crystallography and NMR studies uncovered specific contacts that underlie the potency and selectivity of PCC toward BRD3-BD1 over BRD3-BD2. PCC also displays characteristics of a molecular glue, facilitating proteasome-mediated degradation of BRD3 and BRD4. Finally, PCC is more potent than other withanolide analogues and gold-standard pan-BET inhibitor (+)-JQ1 in cytotoxicity assays across five prostate cancer (PC) cell lines regardless of androgen receptor (AR)-signaling status.


  • Organizational Affiliation

    College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 3121Homo sapiensMutation(s): 0 
Gene Names: BRD3KIAA0043RING3L
UniProt & NIH Common Fund Data Resources
Find proteins for Q15059 (Homo sapiens)
Explore Q15059 
Go to UniProtKB:  Q15059
PHAROS:  Q15059
GTEx:  ENSG00000169925 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15059
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8L6 (Subject of Investigation/LOI)
Query on 8L6

Download Ideal Coordinates CCD File 
B [auth A]Physachenolide C
C30 H42 O9
PLMVDZBEQUQDAZ-NWMHWCAESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.098α = 90
b = 49.316β = 90
c = 60.779γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8L6Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description