7LJE

Discovery of Spirohydantoins as Selective, Orally Bioavailable Inhibitors of p300/CBP Histone Acetyltransferases

• PDB DOI: https://doi.org/10.2210/pdb7LJE/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-01-29 Released: 2021-03-17 
• Deposition Author(s): Jakob, C.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.265 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

Discovery of spirohydantoins as selective, orally bioavailable inhibitors of p300/CBP histone acetyltransferases.

Ji, Z., Clark, R.F., Bhat, V., Matthew Hansen, T., Lasko, L.M., Bromberg, K.D., Manaves, V., Algire, M., Martin, R., Qiu, W., Torrent, M., Jakob, C.G., Liu, H., Cole, P.A., Marmorstein, R., Kesicki, E.A., Lai, A., Michaelides, M.R.

(2021) Bioorg Med Chem Lett 39: 127854-127854

• PubMed: 33631370 
• DOI: https://doi.org/10.1016/j.bmcl.2021.127854
• Primary Citation of Related Structures:  
  7LJE


• PubMed Abstract: 
  

  p300 and CREB-binding protein (CBP) are essential for a multitude of cellular processes. Dysregulation of p300/CBP histone acetyltransferase activity is linked to a broad spectrum of human diseases including cancers. A novel drug-like spirohydantoin (21) has been discovered as a selective orally bioavailable inhibitor of p300/CBP histone acetyltransferase. Lead compound 21 is more potent than the first-in-class lead A-485 in both enzymatic and cellular assays and lacks the off-target inhibition of dopamine and serotonin transporters, that was observed with A-485.

---

Organizational Affiliation: 

Abbvie, Inc. 1 North Waukegan Road, North Chicago, IL-60064, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 163.52 kDa 
• Atom Count: 11,200 
• Modelled Residue Count: 1,286 
• Deposited Residue Count: 1,392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase p300	A, B, C, D	348	Homo sapiens	Mutation(s): 0  Gene Names: EP300, P300 EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens) Go to UniProtKB:  Q09472
PHAROS:  Q09472 GTEx:  ENSG00000100393

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y2P (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	2-[4-[(3'R,4S)-3'-fluoro-1-[2-[(4-fluorophenyl)methyl-[(1S)-2,2,2-trifluoro-1-methyl-ethyl]amino]-2-oxo-ethyl]-2,5-dioxo-spiro[imidazolidine-4,1'-indane]-5'-yl]pyrazol-1-yl]-N-methyl-acetamide C29 H27 F5 N6 O4 SWXCHCQCWFXILM-DAXQEMQKSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Y2P	BindingDB:  7LJE	IC50: min: 6.1, max: 1.31e+4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.265 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.294	α = 90
b = 81.491	β = 117.31
c = 124.095	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Jakob, C.G.

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description