5KU3

BRD4 bromodomain in complex with Cpd59 ((S)-1-(3-((2-fluoro-4-(1-methyl-1H-pyrazol-4-yl)phenyl)amino)-1-(tetrahydrofuran-3-yl)-6,7-dihydro-1H-pyrazolo[4,3-c]pyridin-5(4H)-yl)ethanone)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

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:  
    5KTW, 5KTX, 5KU3, 5KTU

  • 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 initial design targeting the LPF shelf, ZA loop, and acetylated lysine binding regions ...

    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 IC 50 = 0.02 μM, BRET IC 50 = 0.41 μM, BRD4(1) IC 50 = 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A126Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XH
Query on 6XH

Download CCD File 
A
1-[3-[[2-fluoranyl-4-(1-methylpyrazol-4-yl)phenyl]amino]-1-[(3~{S})-oxolan-3-yl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-5-yl]ethanone
C22 H25 F N6 O2
NKOJNOBJGYTLLZ-KRWDZBQOSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6XHIC50:  5490   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.037α = 90
b = 53.115β = 90
c = 106.745γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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