5I1Q

Second bromodomain of TAF1 bound to a pyrrolopyridone compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.6b00264
  • Primary Citation of Related Structures:  
    5I1Q, 5I29, 5I40, 5I7X, 5I7Y, 5I80, 5I88

  • 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 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.


  • 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
Transcription initiation factor TFIID subunit 1144Homo sapiensMutation(s): 0 
Gene Names: TAF1BA2RCCG1CCGSTAF2A
UniProt & NIH Common Fund Data Resources
Find proteins for P21675 (Homo sapiens)
Explore P21675 
Go to UniProtKB:  P21675
PHAROS:  P21675
GTEx:  ENSG00000147133 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21675
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
67C
Query on 67C

Download Ideal Coordinates CCD File 
B [auth A]3-[6-(but-3-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl]-N,N-dimethylbenzamide
C20 H21 N3 O2
VNCNIMOILJQAGJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
67C BindingDB:  5I1Q IC50: min: 46, max: 9900 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.759α = 90
b = 60.042β = 90
c = 60.242γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description