7S3P

BD2 domain of human BRD3 bound to Physachenolide C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 3112Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8L6 (Subject of Investigation/LOI)
Query on 8L6

Download Ideal Coordinates CCD File 
BA [auth J]
L [auth K]
N [auth A]
P [auth B]
Q [auth C]
BA [auth J],
L [auth K],
N [auth A],
P [auth B],
Q [auth C],
S [auth D],
T [auth E],
V [auth F],
W [auth G],
Y [auth H],
Z [auth I]
Physachenolide C
C30 H42 O9
PLMVDZBEQUQDAZ-NWMHWCAESA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth I]
M [auth K]
O [auth A]
R [auth C]
U [auth F]
AA [auth I],
M [auth K],
O [auth A],
R [auth C],
U [auth F],
X [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.448α = 90
b = 158.535β = 90
c = 293.233γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Blu-Icedata collection
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description