6SE4 | pdb_00006se4

Crystal Structure of the first bromodomain of human BRD4 in complex with (+)-JD1, an Organometallic BET Bromodomain Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6SE4/pdb

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


• Deposited: 2019-07-29 Released: 2019-08-14 
• Deposition Author(s): Krojer, T., Hassell-Hart, S., Picaud, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Filippakopoulos, P., Spencer, J., von Delft, F., Structural Genomics Consortium (SGC)
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.179 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the first bromodomain of human BRD4 in complex with (+)-JD1, an Organometallic BET Bromodomain Inhibitor

Krojer, T., Hassell-Hart, S., Picaud, S., Filippakopoulos, P., Spencer, J., von Delft, F.

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: 15.95 kDa 
• Atom Count: 1,307 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L8W (Subject of Investigation/LOI)	C [auth A]	(+)-JD1 C29 H17 Cl Fe N5 O S NJZJPWNUSUAFBI-TXEPZDRESA-N
DMS	E [auth A], F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	B [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.179 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.3063129

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.52	α = 90
b = 43.97	β = 90
c = 79.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-14 
Deposition Author(s): Krojer, T., Hassell-Hart, S., Picaud, S., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Filippakopoulos, P., Spencer, J., von Delft, F., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/P026990/1

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description