6U0D | pdb_00006u0d

Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor ZL0590

• PDB DOI: https://doi.org/10.2210/pdb6U0D/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-14 Released: 2020-08-19 
• Deposition Author(s): Leonard, P.G., Joseph, S.
• Funding Organization(s): Crohns and Colitis Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Discovery, X-ray Crystallography, and Anti-inflammatory Activity of Bromodomain-containing Protein 4 (BRD4) BD1 Inhibitors Targeting a Distinct New Binding Site

Liu, Z., Li, Y., Chen, H., Lai, H., Wang, P., Wu, S., Wold, E.A., Leonard, P.G., Joseph, S., Hu, H., Chiang, C., Brasier, A.R., Tian, B., Zhou, J.

(2022) J Med Chem 

• DOI: https://doi.org/10.1021/acs.jmedchem.1c01851

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.69 kDa 
• Atom Count: 1,290 
• Modeled Residue Count: 126 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POJ (Subject of Investigation/LOI)	C [auth A]	N-[4-({(2S)-2-[(morpholin-4-yl)methyl]pyrrolidin-1-yl}sulfonyl)phenyl]-N'-[4-(trifluoromethyl)phenyl]urea C23 H27 F3 N4 O4 S ZPMULUKHFNMJPF-FQEVSTJZSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
POJ	BindingDB:  6U0D	IC50: min: 90, max: 1093 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.223 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.47	α = 90
b = 42.38	β = 90
c = 80.29	γ = 90

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Leonard, P.G., Joseph, S.

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Funding Organization	Location	Grant Number
Crohns and Colitis Foundation	United States	576144

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 2.0: 2022-01-19
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Refinement description