6AXQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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

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: https://doi.org/10.1021/acs.jmedchem.7b01372
  • Primary Citation of Related Structures:  
    5W0E, 6AXQ, 6AY3, 6AY5

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CREB-binding protein
A, B, C, D
114Homo sapiensMutation(s): 0 
Gene Names: CREBBPCBP
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens)
Go to UniProtKB:  Q92793
PHAROS:  Q92793
GTEx:  ENSG00000005339 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2Y
Query on C2Y

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
L [auth C],
N [auth D]
methyl 1H-indole-3-carboxylate
C10 H9 N O2
QXAUTQFAWKKNLM-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
J [auth C]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
J [auth C],
K [auth C],
M [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
C2Y BindingDB:  6AXQ IC50: 9.90e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.71α = 90
b = 69.98β = 90
c = 110.28γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description