8FV2

Bromodomain of CBP liganded with CCS-1477


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41467-024-47102-0
  • Primary Citation of 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.


  • Organizational Affiliation

    Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CREB-binding protein
A, B, C, D
116Homo sapiensMutation(s): 0 
Gene Names: CREBBPCBP
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens)
Explore Q92793 
Go to UniProtKB:  Q92793
PHAROS:  Q92793
GTEx:  ENSG00000005339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92793
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JHL (Subject of Investigation/LOI)
Query on JHL

Download Ideal Coordinates CCD File 
F [auth A]
L [auth B]
M [auth B]
N [auth C]
O [auth C]
F [auth A],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth D]
(6S)-1-[3,4-bis(fluoranyl)phenyl]-6-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-(4-methoxycyclohexyl)benzimidazol-2-yl]piperidin-2-one
C30 H32 F2 N4 O3
SKDNDJWEBPQKCS-CLHVYKLBSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
K [auth B],
Q [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JHL BindingDB:  8FV2 Kd: 14 (nM) from 1 assay(s)
IC50: 2.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.453α = 90
b = 79.453β = 90
c = 97.127γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

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