6WW8

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.235
R-Value Work: 0.193
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-020-0181-z
Primary Citation of Related Structures:
6WW8

Organizational Affiliation

Division of Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA USA.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60885
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YR0 (Subject of Investigation/LOI) Query on YR0 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.235
R-Value Work: 0.193
R-Value Observed: 0.197
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

Kutateladze, T.G.

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

Revision History (Full details and data files)

Version 1.0: 2020-08-26
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.