6WW8 | pdb_00006ww8

BRD4 Bromodomain 1 in complex with triple CDK4/6-PI3K-BET inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6WW8/pdb

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


• Deposited: 2020-05-08 Released: 2020-08-26 
• Deposition Author(s): Vann, K.R., Kutateladze, T.G.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

A triple action CDK4/6-PI3K-BET inhibitor with augmented cancer cell cytotoxicity.

Burgoyne, A.M., Vann, K.R., Joshi, S., Morales, G.A., Vega, F.M., Singh, A., Pal, D., Merati, A.B., Kutateladze, T.G., Durden, D.L.

(2020) Cell Discov 6: 49-49

• PubMed: 32793389 
• DOI: https://doi.org/10.1038/s41421-020-0181-z
• Primary Citation Related Structures: 
  6WW8

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Organizational Affiliation: 
• Division of Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA USA.
Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO USA.
Division of Pediatric Hematology and Oncology, Department of Pediatrics, Moores Cancer Center, University of California San Diego, La Jolla, CA USA.
SignalRx Pharmaceuticals, San Diego, CA USA.
Department of Cell Biology, Instituto de Biomedicina de Sevilla, Universidad de Sevilla, Sevilla, Spain.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.85 kDa 
• Atom Count: 1,177 
• Modeled Residue Count: 131 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	138	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YR0 (Subject of Investigation/LOI)	B [auth A]	7-cyclopentyl-N,N-dimethyl-2-({4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]phenyl}amino)-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide C31 H32 N6 O4 S XJKTXWSMMWPNTP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.318	α = 90
b = 45.318	β = 90
c = 61.895	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Vann, K.R., Kutateladze, T.G.

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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: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description