4LYS | pdb_00004lys

Crystal Structure of BRD4(1) bound to Colchiceine

• PDB DOI: https://doi.org/10.2210/pdb4LYS/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: 1.83 Å
• R-Value Free: 
  0.267 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

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 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.

Macromolecule Content 

• Total Structure Weight: 15.44 kDa 
• Atom Count: 1,188 
• Modeled Residue Count: 124 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	126	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2SJ	D [auth A]	N-[(7S)-10-hydroxy-1,2,3-trimethoxy-9-oxo-5,6,7,9-tetrahydrobenzo[a]heptalen-7-yl]acetamide C21 H23 N O6 PRGILOMAMBLWNG-HNNXBMFYSA-N
NA	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.267 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.047	α = 90
b = 108.072	β = 90
c = 30.464	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

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: 2014-01-29
  Changes: Non-polymer description, Structure summary
• Version 1.2: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary