8FXE | pdb_00008fxe

Bromodomain of CBP liganded with iCBP6

• PDB DOI: https://doi.org/10.2210/pdb8FXE/pdb

• Classification: TRANSCRIPTION/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-24 Released: 2024-02-07 
• Deposition Author(s): Schonbrunn, E., Bikowitz, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Group 3 medulloblastoma transcriptional networks collapse under domain specific EP300/CBP inhibition.

Shendy, N.A.M., Bikowitz, M., Sigua, L.H., Zhang, Y., Mercier, A., Khashana, Y., Nance, S., Liu, Q., Delahunty, I.M., Robinson, S., Goel, V., Rees, M.G., Ronan, M.A., Wang, T., Kocak, M., Roth, J.A., Wang, Y., Freeman, B.B., Orr, B.A., Abraham, B.J., Roussel, M.F., Schonbrunn, E., Qi, J., Durbin, A.D.

(2024) Nat Commun 15: 3483-3483

• PubMed: 38664416 
• DOI: https://doi.org/10.1038/s41467-024-47102-0
• Primary Citation Related Structures: 
  8FV2, 8FVF, 8FVK, 8FVS, 8FXA, 8FXE, 8FXO, 8G6T, 8GA2


• PubMed Abstract: 
  

  Chemical discovery efforts commonly target individual protein domains. Many proteins, including the EP300/CBP histone acetyltransferases (HATs), contain several targetable domains. EP300/CBP are critical gene-regulatory targets in cancer, with existing high potency inhibitors of either the catalytic HAT domain or protein-binding bromodomain (BRD). A domain-specific inhibitory approach to multidomain-containing proteins may identify exceptional-responding tumor types, thereby expanding a therapeutic index. Here, we discover that targeting EP300/CBP using the domain-specific inhibitors, A485 (HAT) or CCS1477 (BRD) have different effects in select tumor types. Group 3 medulloblastoma (G3MB) cells are especially sensitive to BRD, compared with HAT inhibition. Structurally, these effects are mediated by the difluorophenyl group in the catalytic core of CCS1477. Mechanistically, bromodomain inhibition causes rapid disruption of genetic dependency networks that are required for G3MB growth. These studies provide a domain-specific structural foundation for drug discovery efforts targeting EP300/CBP and identify a selective role for the EP300/CBP bromodomain in maintaining genetic dependency networks in G3MB.

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Organizational Affiliation: 
• Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, USA.
Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Tumor Cell Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA.
The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Preclinical Pharmacokinetics Shared Resource, St Jude Children's Research Hospital, Memphis, TN, USA.
Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA.
Drug Discovery Department, Moffitt Cancer Center, Tampa, FL, USA. [e-mail].
Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA. [e-mail].
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. [e-mail].
Department of Medicine, Harvard Medical School, Boston, MA, USA. [e-mail].
Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 14.9 kDa 
• Atom Count: 1,239 
• Modeled Residue Count: 119 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	A	119	Homo sapiens	Mutation(s): 0  Gene Names: CREBBP, CBP EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens) Explore Q92793  Go to UniProtKB:  Q92793
PHAROS:  Q92793 GTEx:  ENSG00000005339

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YID (Subject of Investigation/LOI)	B [auth A]	(6S)-1-(3-tert-butylphenyl)-6-{(5P)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1s,4R)-4-methoxycyclohexyl]-1H-benzimidazol-2-yl}piperidin-2-one C34 H42 N4 O3 AITZELJGZIFAPE-NSROOHRNSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.77	α = 90
b = 49.54	β = 90
c = 80.73	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Schonbrunn, E., Bikowitz, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 1.1: 2024-06-05
  Changes: Database references