5W0F

CREBBP Bromodomain in complex with Cpd3 ((S)-1-(3-(6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl)-1-(tetrahydrofuran-3-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl)ethan-1-one)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

GNE-781, A Highly Advanced Potent and Selective Bromodomain Inhibitor of Cyclic Adenosine Monophosphate Response Element Binding Protein, Binding Protein (CBP).

Romero, F.A.Murray, J.Lai, K.W.Tsui, V.Albrecht, B.K.An, L.Beresini, M.H.de Leon Boenig, G.Bronner, S.M.Chan, E.W.Chen, K.X.Chen, Z.Choo, E.F.Clagg, K.Clark, K.Crawford, T.D.Cyr, P.de Almeida Nagata, D.Gascoigne, K.E.Grogan, J.L.Hatzivassiliou, G.Huang, W.Hunsaker, T.L.Kaufman, S.Koenig, S.G.Li, R.Li, Y.Liang, X.Liao, J.Liu, W.Ly, J.Maher, J.Masui, C.Merchant, M.Ran, Y.Taylor, A.M.Wai, J.Wang, F.Wei, X.Yu, D.Zhu, B.Y.Zhu, X.Magnuson, S.

(2017) J Med Chem 60: 9162-9183

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00796
  • Primary Citation of Related Structures:  
    5W0F, 5W0I, 5W0L, 5W0Q

  • PubMed Abstract: 

    Inhibition of the bromodomain of the transcriptional regulator CBP/P300 is an especially interesting new therapeutic approach in oncology. We recently disclosed in vivo chemical tool 1 (GNE-272) for the bromodomain of CBP that was moderately potent and selective over BRD4(1). In pursuit of a more potent and selective CBP inhibitor, we used structure-based design. Constraining the aniline of 1 into a tetrahydroquinoline motif maintained potency and increased selectivity 2-fold. Structure-activity relationship studies coupled with further structure-based design targeting the LPF shelf, BC loop, and KAc regions allowed us to significantly increase potency and selectivity, resulting in the identification of non-CNS penetrant 19 (GNE-781, TR-FRET IC 50 = 0.94 nM, BRET IC 50 = 6.2 nM; BRD4(1) IC 50 = 5100 nΜ) that maintained good in vivo PK properties in multiple species. Compound 19 displays antitumor activity in an AML tumor model and was also shown to decrease Foxp3 transcript levels in a dose dependent manner.


  • 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 protein148Homo sapiensMutation(s): 0 
Gene Names: CREBBPCBP
EC: 2.3.1.48
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9U7
Query on 9U7

Download Ideal Coordinates CCD File 
B [auth A]1-{3-[6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl]-1-[(3S)-oxolan-3-yl]-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl}ethan-1-one
C25 H30 N6 O2
OTJPVMSGEHNVNV-NRFANRHFSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9U7 BindingDB:  5W0F IC50: min: 16, max: 320 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.195α = 90
b = 48.256β = 90
c = 80.502γ = 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

  • Released Date: 2018-03-07 
  • Deposition Author(s): Murray, J.M.

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description