6P38 | pdb_00006p38

Crystal Structure Analysis of TAF1 Bromodomain

• PDB DOI: https://doi.org/10.2210/pdb6P38/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-23 Released: 2020-05-27 
• Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.219 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Dual Inhibition of TAF1 and BET Bromodomains from the BI-2536 Kinase Inhibitor Scaffold.

Remillard, D., Buckley, D.L., Seo, H.S., Ferguson, F.M., Dhe-Paganon, S., Bradner, J.E., Gray, N.S.

(2019) ACS Med Chem Lett 10: 1443-1449

• PubMed: 31620231 
• DOI: https://doi.org/10.1021/acsmedchemlett.9b00243
• Primary Citation Related Structures: 
  6P38


• PubMed Abstract: 
  

  Recent reports have highlighted the dual bromodomains of TAF1 (TAF1(1,2)) as synergistic with BET inhibition in cellular cancer models, engendering interest in TAF/BET polypharmacology. Here, we examine structure activity relationships within the BI-2536 PLK1 kinase inhibitor scaffold, previously reported to bind BRD4. We examine binding by this ligand to TAF1(2) and apply structure guided design strategies to discriminate binding to both the PLK1 kinase and BRD4(1) bromodomain while retaining activity on TAF1(2). Through this effort we discover potent dual inhibitors of TAF1(2)/BRD4(1), as well as biased derivatives showing marked TAF1 selectivity. We resolve X-ray crystallographic data sets to examine the mechanisms of the observed TAF1 selectivity and to provide a resource for further development of this scaffold.

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Organizational Affiliation: 
• Department of Cancer Biology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States.
Department of Medical Oncology, Dana Farber Cancer Institute, Boston Massachusetts 02115, United States.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston Massachusetts 02115, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.42 kDa 
• Atom Count: 1,077 
• Modeled Residue Count: 128 
• Deposited Residue Count: 137 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor TFIID subunit 1	A	137	Homo sapiens	Mutation(s): 0  Gene Names: TAF1, BA2R, CCG1, CCGS, TAF2A EC: 2.3.1.48 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P21675 (Homo sapiens) Explore P21675  Go to UniProtKB:  P21675
PHAROS:  P21675 GTEx:  ENSG00000147133

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NQV (Subject of Investigation/LOI)	B [auth A]	4-{[(3R)-4-cyclopentyl-1,3-dimethyl-2-oxo-1,2,3,4-tetrahydropyrido[2,3-b]pyrazin-6-yl]amino}-N-(1-methylpiperidin-4-yl)-3-[(propan-2-yl)oxy]benzamide C30 H42 N6 O3 AGCMTUNUCHFYSQ-HXUWFJFHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NQV	BindingDB:  6P38	IC50: 89 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.219 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.89	α = 90
b = 95.89	β = 90
c = 94.22	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
xia2	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-12-09
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description