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.

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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 

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

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Organizational Affiliation: 

Pharmazeutische Bioinformatik, Institut für Pharmazeutische, Wissenschaften, Albert-Ludwigs-Universität, Hermann-Herder-Strasse 9, 79104 Freiburg (Germany) http://www.pharmaceutical-bioinformatics.org.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
21Q	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

Binding Affinity Annotations
ID	Source	Binding Affinity
21Q	BindingDB:  4LYW	Kd: min: 160, max: 240 (nM) from 2 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

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Wohlwend, D., Gerhardt, S., Einsle, O.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations