Macromolecule Content

Total Structure Weight: 15.5 kDa
Atom Count: 1,206
Modelled Residue Count: 127
Deposited Residue Count: 127
Unique protein chains: 1

4LYW

Crystal Structure of BRD4(1) bound to inhibitor XD14

PDB DOI: https://doi.org/10.2210/pdb4LYW/pdb

Classification: PROTEIN BINDING/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-07-31 Released: 2014-01-15
Deposition Author(s): Wohlwend, D., Gerhardt, S., Einsle, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.235
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

4-Acyl pyrroles: mimicking acetylated lysines in histone code reading.

Lucas, X., Wohlwend, D., Hugle, M., Schmidtkunz, K., Gerhardt, S., Schule, R., Jung, M., Einsle, O., Gunther, S.

(2013) Angew Chem Int Ed Engl 52: 14055-14059

PubMed: 24272870 Search on PubMed
DOI: https://doi.org/10.1002/anie.201307652
Primary Citation of Related Structures:
4LYI, 4LYS, 4LYW, 4LZR, 4LZS

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	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60885
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
21Q Query on 21Q Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	4-acetyl-N-[5-(diethylsulfamoyl)-2-hydroxyphenyl]-3-ethyl-5-methyl-1H-pyrrole-2-carboxamide C₂₀ H₂₇ N₃ O₅ S DPBKLIVPNYGQQG-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
21Q	BindingDB: 4LYW	Kd: 240 (nM) from 1 assay(s)
21Q	Binding MOAD: 4LYW	Kd: 237 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.235
R-Value Work: 0.197
R-Value Observed: 0.199
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.81	α = 90
b = 47.92	β = 90
c = 57.8	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release

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.