5KTU

Crystal structure of the bromodomain of human CREBBP bound to pyrazolopiperidine scaffold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Potent and Selective in Vivo Probe (GNE-272) for the Bromodomains of CBP/EP300.

Crawford, T.D.Romero, F.A.Lai, K.W.Tsui, V.Taylor, A.M.de Leon Boenig, G.Noland, C.L.Murray, J.Ly, J.Choo, E.F.Hunsaker, T.L.Chan, E.W.Merchant, M.Kharbanda, S.Gascoigne, K.E.Kaufman, S.Beresini, M.H.Liao, J.Liu, W.Chen, K.X.Chen, Z.Conery, A.R.Cote, A.Jayaram, H.Jiang, Y.Kiefer, J.R.Kleinheinz, T.Li, Y.Maher, J.Pardo, E.Poy, F.Spillane, K.L.Wang, F.Wang, J.Wei, X.Xu, Z.Xu, Z.Yen, I.Zawadzke, L.Zhu, X.Bellon, S.Cummings, R.Cochran, A.G.Albrecht, B.K.Magnuson, S.

(2016) J. Med. Chem. 59: 10549-10563

  • DOI: 10.1021/acs.jmedchem.6b01022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The single bromodomain of the closely related transcriptional regulators CBP/EP300 is a target of much recent interest in cancer and immune system regulation. A co-crystal structure of a ligand-efficient screening hit and the CBP bromodomain guided i ...

    The single bromodomain of the closely related transcriptional regulators CBP/EP300 is a target of much recent interest in cancer and immune system regulation. A co-crystal structure of a ligand-efficient screening hit and the CBP bromodomain guided initial design targeting the LPF shelf, ZA loop, and acetylated lysine binding regions. Structure-activity relationship studies allowed us to identify a more potent analogue. Optimization of permeability and microsomal stability and subsequent improvement of mouse hepatocyte stability afforded 59 (GNE-272, TR-FRET IC50 = 0.02 μM, BRET IC50 = 0.41 μM, BRD4(1) IC50 = 13 μM) that retained the best balance of cell potency, selectivity, and in vivo PK. Compound 59 showed a marked antiproliferative effect in hematologic cancer cell lines and modulates MYC expression in vivo that corresponds with antitumor activity in an AML tumor model.


    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
118Homo 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
6XB
Query on 6XB

Download SDF File 
Download CCD File 
A
1-(3-phenylazanyl-1,4,6,7-tetrahydropyrazolo[4,3-c]pyridin-5-yl)ethanone
C14 H16 N4 O
ZXIJCVCJLDGJRX-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 125.220α = 90.00
b = 125.220β = 90.00
c = 39.789γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references