7RUH

Bromodomain-containing protein 4 (BRD4) bromodomain 2 (BD2) complexed with XR844

PDB DOI: https://doi.org/10.2210/pdb7RUH/pdb

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

Deposited: 2021-08-17 Released: 2022-08-24
Deposition Author(s): Ratia, K.M., Xiong, R., Li, Y., Shen, Z., Zhao, J., Huang, F., Dubrovyskyii, O., Thatcher, G.R.
Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.218
R-Value Work: 0.183
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Bromodomain-containing protein 4 (BRD4) bromodomain 2 (BD2) complexed with XR844

Xiong, R., Ratia, K.M., Li, Y., Shen, Z., Zhao, J., Huang, F., Dubrovyskyii, O., Thatcher, G.R.

To be published.

Macromolecule Content

Total Structure Weight: 15.93 kDa
Atom Count: 1,042
Modelled Residue Count: 113
Deposited Residue Count: 130
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	130	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
7QZ (Subject of Investigation/LOI) Query on 7QZ Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-{1-[1,1-di(pyridin-2-yl)ethyl]-6-(5-{[(2-fluorophenyl)carbamoyl]amino}-1-methyl-6-oxo-1,6-dihydropyridin-3-yl)-1H-indol-4-yl}-2,2,2-trifluoroethane-1-sulfonamide C₃₅ H₂₉ F₄ N₇ O₄ S RFUGSFUWHIKRES-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.218
R-Value Work: 0.183
R-Value Observed: 0.185
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.98	α = 90
b = 53.168	β = 90
c = 72.481	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Dubrovyskyii, O.

Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	UL1RR029879

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, 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.