8FV2 | pdb_00008fv2

Bromodomain of CBP liganded with CCS-1477


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.226 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8FV2

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 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.

Macromolecule Content 

  • Total Structure Weight: 59.2 kDa 
  • Atom Count: 4,673 
  • Modeled Residue Count: 461 
  • Deposited Residue Count: 464 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.226 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
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