6LG5

Crystal Structure of the first bromodomain of human BRD4 in complex with compound BDF-1038

PDB DOI: https://doi.org/10.2210/pdb6LG5/pdb

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

Deposited: 2019-12-04 Released: 2020-12-09
Deposition Author(s): Xu, H., Zuo, Y., Zhang, H.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.202
R-Value Work: 0.176
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Lead-Opt: An efficient tool for structural optimization of lead compounds

Xu, H., Zuo, Y.

To be published.

Macromolecule Content

Total Structure Weight: 15.16 kDa
Atom Count: 1,209
Modelled Residue Count: 124
Deposited Residue Count: 125
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	125	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
EC3 (Subject of Investigation/LOI) Query on EC3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	1-[(5-chloranyl-8-oxidanyl-quinolin-7-yl)methyl]pyrrolidin-2-one C₁₄ H₁₃ Cl N₂ O₂ YWICHOLVOTVAMW-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: 1.83 Å
R-Value Free: 0.202
R-Value Work: 0.176
R-Value Observed: 0.178
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.964	α = 90
b = 47.246	β = 90
c = 78.897	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81903538

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2023-11-22
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.