7REL

Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with dual BRD4-JAK2 inhibitor MA9-060

PDB DOI: https://doi.org/10.2210/pdb7REL/pdb

Classification: GENE REGULATION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-13 Released: 2021-07-21
Deposition Author(s): Karim, M.R., Schonbrunn, E.
Funding Organization(s): Leukemia & Lymphoma Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.191
R-Value Work: 0.163
R-Value Observed: 0.164

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with dual BRD4-JAK2 inhibitor MA9-060

Karim, M.R., Schonbrunn, E.

To be published.

Macromolecule Content

Total Structure Weight: 15.72 kDa
Atom Count: 1,287
Modelled Residue Count: 127
Deposited Residue Count: 127
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	127	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4OW (Subject of Investigation/LOI) Query on 4OW Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-[2-chloro-5-({2-[3-fluoro-4-(1-methylpiperidin-4-yl)anilino]-5-methylpyrimidin-4-yl}amino)phenyl]-2-methylpropane-2-sulfonamide C₂₇ H₃₄ Cl F N₆ O₂ S FPGNUYNSOYSDAN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-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: 1.55 Å
R-Value Free: 0.191
R-Value Work: 0.163
R-Value Observed: 0.164
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.1	α = 90
b = 44.159	β = 90
c = 78.888	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Leukemia & Lymphoma Society	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-07-21
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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.