5I29

TAF1(2) bound to a pyrrolopyridone compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains.

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

(2016) J.Med.Chem. 59: 5391-5402

  • DOI: 10.1021/acs.jmedchem.6b00264
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biological role played by non-BET bromodomains remains poorly understood, and it is therefore imperative to identify potent and highly selective inhibitors to effectively explore the biology of individual bromodomain proteins. A ligand-efficient ...

    The biological role played by non-BET bromodomains remains poorly understood, and it is therefore imperative to identify potent and highly selective inhibitors to effectively explore the biology of individual bromodomain proteins. A ligand-efficient nonselective bromodomain inhibitor was identified from a 6-methyl pyrrolopyridone fragment. Small hydrophobic substituents replacing the N-methyl group were designed directing toward the conserved bromodomain water pocket, and two distinct binding conformations were then observed. The substituents either directly displaced and rearranged the conserved solvent network, as in BRD4(1) and TAF1(2), or induced a narrow hydrophobic channel adjacent to the lipophilic shelf, as in BRD9 and CECR2. The preference of distinct substituents for individual bromodomains provided selectivity handles useful for future lead optimization efforts for selective BRD9, CECR2, and TAF1(2) inhibitors.


    Related Citations: 
    • A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications.
      Flynn, E.M.,Huang, O.W.,Poy, F.,Oppikofer, M.,Bellon, S.F.,Tang, Y.,Cochran, A.G.
      (2015) Structure 23: 1801


    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
Transcription initiation factor TFIID subunit 1
A
144Homo sapiensMutation(s): 0 
Gene Names: TAF1 (BA2R, CCG1, CCGS, TAF2A)
EC: 2.3.1.48, 2.7.11.1
Find proteins for P21675 (Homo sapiens)
Go to Gene View: TAF1
Go to UniProtKB:  P21675
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
67B
Query on 67B

Download SDF File 
Download CCD File 
A
N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)benzamide
C17 H17 N3 O2
YHMNROQTPUKNLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
67BIC50: 59 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.397α = 90.00
b = 59.471β = 90.00
c = 59.866γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references