7RUH | pdb_00007ruh

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 (Depositor), 0.228 (DCC)
R-Value Work:
0.183 (Depositor), 0.197 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 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
Modeled Residue Count: 113
Deposited Residue Count: 130
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.228 (DCC)
R-Value Work: 0.183 (Depositor), 0.197 (DCC)
R-Value Observed: 0.185 (Depositor)

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

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Ligand Structure Quality Assessment

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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
Version 1.2: 2024-11-06
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.