7DPN

Crystal structure of BRD2(BD1)with ligand ZB-BD-224 bound

• PDB DOI: https://doi.org/10.2210/pdb7DPN/pdb

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


• Deposited: 2020-12-20 Released: 2021-12-22 
• Deposition Author(s): Li, Z., Lu, T., Chen, P., Luo, C., Zhou, B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Structure Base Design of A new chemotype of Four-Cycle Compounds as Bromodomain and Extra-Terminal (BET) Inhibitors with The Second Bromodomain Bias and Highly Anti-inflammatory Potency

Li, Z., Lu, T., Chen, P., Luo, C., Zgou, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 44.41 kDa 
• Atom Count: 3,123 
• Modelled Residue Count: 327 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B, C	122	Homo sapiens	Mutation(s): 0  Gene Names: BRD2, KIAA9001, RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440  Go to UniProtKB:  P25440
PHAROS:  P25440 GTEx:  ENSG00000204256

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HFU (Subject of Investigation/LOI)	D [auth A], E [auth B]	5-(1-naphthoyl)-11-methyl-8-((methylsulfonyl)methyl)-4,5-dihydro-2,3a1,5-triazadibenzo[cd,h]azulen-1(2H)-one C28 H23 N3 O4 S SVWVGWHDUPYUFQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.219 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.784	α = 90
b = 55.778	β = 94.245
c = 68.098	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Li, Z., Lu, T., Chen, P., Luo, C., Zhou, B.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	91853205
National Natural Science Foundation of China (NSFC)	China	81625022
National Natural Science Foundation of China (NSFC)	China	81821005

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description