6DF4

TAF1-BD2 in complex with Cpd8 (6-(but-3-en-1-yl)-4-(3-(morpholine-4-carbonyl)phenyl)-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

GNE-371, a Potent and Selective Chemical Probe for the Second Bromodomains of Human Transcription-Initiation-Factor TFIID Subunit 1 and Transcription-Initiation-Factor TFIID Subunit 1-like.

Wang, S.Tsui, V.Crawford, T.D.Audia, J.E.Burdick, D.J.Beresini, M.H.Cote, A.Cummings, R.Duplessis, M.Flynn, E.M.Hewitt, M.C.Huang, H.R.Jayaram, H.Jiang, Y.Joshi, S.Murray, J.Nasveschuk, C.G.Pardo, E.Poy, F.Romero, F.A.Tang, Y.Taylor, A.M.Wang, J.Xu, Z.Zawadzke, L.E.Zhu, X.Albrecht, B.K.Magnuson, S.R.Bellon, S.Cochran, A.G.

(2018) J. Med. Chem. 61: 9301-9315

  • DOI: 10.1021/acs.jmedchem.8b01225
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biological functions of the dual bromodomains of human transcription-initiation-factor TFIID subunit 1 (TAF1(1,2)) remain unknown, although TAF1 has been identified as a potential target for oncology research. Here, we describe the discovery of a ...

    The biological functions of the dual bromodomains of human transcription-initiation-factor TFIID subunit 1 (TAF1(1,2)) remain unknown, although TAF1 has been identified as a potential target for oncology research. Here, we describe the discovery of a potent and selective in vitro tool compound for TAF1(2), starting from a previously reported lead. A cocrystal structure of lead compound 2 bound to TAF1(2) enabled structure-based design and structure-activity-relationship studies that ultimately led to our in vitro tool compound, 27 (GNE-371). Compound 27 binds TAF1(2) with an IC 50 of 10 nM while maintaining excellent selectivity over other bromodomain-family members. Compound 27 is also active in a cellular-TAF1(2) target-engagement assay (IC 50 = 38 nM) and exhibits antiproliferative synergy with the BET inhibitor JQ1, suggesting engagement of endogenous TAF1 by 27 and further supporting the use of 27 in mechanistic and target-validation studies.


    Organizational Affiliation

    Constellation Pharmaceuticals , 215 First Street, Suite 200 , Cambridge , Massachusetts 02142 , United States.,Wuxi Apptec Company, Ltd. , 288 Fute Zhong Road , Waigaoqiao Free Trade Zone, Shanghai 200131 , People's Republic of China.,Genentech Inc. , 1 DNA Way , South San Francisco , California 94080 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor TFIID subunit
A
167Oryctolagus cuniculusMutation(s): 0 
Gene Names: TAF1
Find proteins for U3KMH2 (Oryctolagus cuniculus)
Go to Gene View: TAF1
Go to UniProtKB:  U3KMH2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G9Y
Query on G9Y

Download SDF File 
Download CCD File 
A
6-(but-3-en-1-yl)-4-[3-(morpholine-4-carbonyl)phenyl]-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one
C22 H23 N3 O3
SMABWKWHQKFGDR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.808α = 90.00
b = 59.654β = 90.00
c = 60.579γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
AutoProcessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-05-14 
  • Released Date: 2018-10-31 
  • Deposition Author(s): Murray, J.M., Tang, Y.

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-11-14
    Type: Data collection, Database references