6YIN | pdb_00006yin

Crystal structure of the first bromodomain of BRD4 in complex with a benzo-diazepine ligand

• PDB DOI: https://doi.org/10.2210/pdb6YIN/pdb

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


• Deposited: 2020-04-01 Released: 2020-04-15 
• Deposition Author(s): Picaud, S., Brand, M., Tobias, K., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Conway, S., Filippakopoulos, P.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.245 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the first bromodomain of BRD4 in complex with a benzo-diazepine ligand

Picaud, S., Brand, M., Tobias, K., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Conway, S., Filippakopoulos, P.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.52 kDa 
• Atom Count: 1,151 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OS8 (Subject of Investigation/LOI)	B [auth A]	(4~{R})-~{N}-[3-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)propyl]-4-methyl-2-oxidanylidene-1,3,4,5-tetrahydro-1,5-benzodiazepine-6-carboxamide C24 H30 N4 O3 XZQSPHYHBYGJPB-MRXNPFEDSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OS8	BindingDB:  6YIN	Kd: min: 2820, max: 5800 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.245 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.603	α = 90
b = 48.347	β = 90
c = 58.962	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Picaud, S., Brand, M., Tobias, K., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Conway, S., Filippakopoulos, P.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N010051/1

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description