7YL2 | pdb_00007yl2

Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y07004

• PDB DOI: https://doi.org/10.2210/pdb7YL2/pdb

• Classification: ANTITUMOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-07-25 Released: 2023-07-26 
• Deposition Author(s): Huang, Y., Wei, A., Dong, R., Xu, H., Zhang, C., Chen, Z., Li, J., Wu, X., Zhang, Y., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.204 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y07004

Huang, Y., Wei, A., Dong, R., Xu, H., Zhang, C., Chen, Z., Li, J., Wu, X., Zhang, Y., Xu, Y.

To be published.

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: 17.24 kDa 
• Atom Count: 1,214 
• Modeled Residue Count: 133 
• Deposited Residue Count: 141 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	141	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JCO (Subject of Investigation/LOI)	B [auth A]	N-(1-ethyl-2-oxidanylidene-3H-indol-5-yl)cyclohexanesulfonamide C16 H22 N2 O3 S OTQKWYLWWLILAL-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3	D [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.204 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.18	α = 90
b = 50.52	β = 90
c = 52.88	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Huang, Y., Wei, A., Dong, R., Xu, H., Zhang, C., Chen, Z., Li, J., Wu, X., Zhang, Y., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81673357

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary