6AXQ

CREBBP bromodomain in complex with Cpd6 (methyl 1H-indole-3-carboxylate)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A Unique Approach to Design Potent and Selective Cyclic Adenosine Monophosphate Response Element Binding Protein, Binding Protein (CBP) Inhibitors.

Bronner, S.M.Murray, J.Romero, F.A.Lai, K.W.Tsui, V.Cyr, P.Beresini, M.H.de Leon Boenig, G.Chen, Z.Choo, E.F.Clark, K.R.Crawford, T.D.Jayaram, H.Kaufman, S.Li, R.Li, Y.Liao, J.Liang, X.Liu, W.Ly, J.Maher, J.Wai, J.Wang, F.Zheng, A.Zhu, X.Magnuson, S.

(2017) J. Med. Chem. 60: 10151-10171

  • DOI: 10.1021/acs.jmedchem.7b01372
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The epigenetic regulator CBP/P300 presents a novel therapeutic target for oncology. Previously, we disclosed the development of potent and selective CBP bromodomain inhibitors by first identifying pharmacophores that bind the KAc region and then buil ...

    The epigenetic regulator CBP/P300 presents a novel therapeutic target for oncology. Previously, we disclosed the development of potent and selective CBP bromodomain inhibitors by first identifying pharmacophores that bind the KAc region and then building into the LPF shelf. Herein, we report the "hybridization" of a variety of KAc-binding fragments with a tetrahydroquinoline scaffold that makes optimal interactions with the LPF shelf, imparting enhanced potency and selectivity to the hybridized ligand. To demonstrate the utility of our hybridization approach, two analogues containing unique Asn binders and the optimized tetrahydroquinoline moiety were rapidly optimized to yield single-digit nanomolar inhibitors of CBP with exquisite selectivity over BRD4(1) and the broader bromodomain family.


    Organizational Affiliation

    Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CREB-binding protein
A, B, C, D
114Homo sapiensMutation(s): 0 
Gene Names: CREBBP (CBP)
EC: 2.3.1.48
Find proteins for Q92793 (Homo sapiens)
Go to Gene View: CREBBP
Go to UniProtKB:  Q92793
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2Y
Query on C2Y

Download SDF File 
Download CCD File 
A, B, C, D
methyl 1H-indole-3-carboxylate
C10 H9 N O2
QXAUTQFAWKKNLM-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B, C, D
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.200 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 68.710α = 90.00
b = 69.980β = 90.00
c = 110.280γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release