5XI3 | pdb_00005xi3

BRD4 bound with compound Bdi3

PDB DOI: https://doi.org/10.2210/pdb5XI3/pdb

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

Deposited: 2017-04-25 Released: 2018-05-02
Deposition Author(s): Xiong, B., Cao, D., Li, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.218 (Depositor), 0.191 (DCC)
R-Value Work:
0.187 (Depositor)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5XI3

Ligand Structure Quality Assessment

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

Literature

BRD4 bound with compound Bdi3

Xiong, B., Cao, D., Li, Y.

To be published.

Macromolecule Content

Total Structure Weight: 15.09 kDa
Atom Count: 1,197
Modeled Residue Count: 124
Deposited Residue Count: 124
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	124	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
8F6 Query on 8F6 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]	(3~{R})-4-cyclopropyl-1,3-dimethyl-6-[[(1~{R})-1-phenylethyl]amino]-3~{H}-quinoxalin-2-one C₂₁ H₂₅ N₃ O YJXOISPYJORRTP-HUUCEWRRSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.218 (Depositor), 0.191 (DCC)
R-Value Work: 0.187 (Depositor)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.478	α = 90
b = 47.581	β = 90
c = 78.714	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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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.