6DB0

N-Terminal bromodomain of Human BRD2 with a Tetrahydroquinoline analogue

• PDB DOI: https://doi.org/10.2210/pdb6DB0/pdb

• Classification: Transcription/Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-05-02 Released: 2019-11-13 
• Deposition Author(s): White, S.W., Yun, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.188 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Starting Model: experimental

Literature

N-Terminal bromodomain of Human BRD2 with a Tetrahydroquinoline analogue

White, S.W., Yun, M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.61 kDa 
• Atom Count: 3,031 
• Modelled Residue Count: 331 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B, C	138	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G3J (Subject of Investigation/LOI)	E [auth A], F [auth B]	1-[(2S,4R)-4-[(2-chlorophenyl)amino]-2-methyl-6-(1H-pyrazol-3-yl)-3,4-dihydroquinolin-1(2H)-yl]ethan-1-one C21 H21 Cl N4 O XRGFSBWBLFRFEN-RNODOKPDSA-N
EPE	G [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	H [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.188 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.316	α = 90
b = 55.796	β = 94.58
c = 68.363	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-13 
Deposition Author(s): White, S.W., Yun, M.

Revision History  

• Version 1.0: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description