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: 13.3 kDa 
• Atom Count: 1,009 
• Modelled Residue Count: 109 
• Deposited Residue Count: 109 
• Unique protein chains: 1

 5UEX

BRD4_BD2_A-1497627

• PDB DOI:  https://doi.org/10.2210/pdb5UEX/pdb

• Classification: SIGNALING PROTEIN/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2017-01-03 Released: 2017-05-10 
• Deposition Author(s): Park, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.279 
• R-Value Work: 0.236 
• R-Value Observed: 0.238 

Literature

Fragment-Based, Structure-Enabled Discovery of Novel Pyridones and Pyridone Macrocycles as Potent Bromodomain and Extra-Terminal Domain (BET) Family Bromodomain Inhibitors.

Wang, L., Pratt, J.K., Soltwedel, T., Sheppard, G.S., Fidanze, S.D., Liu, D., Hasvold, L.A., Mantei, R.A., Holms, J.H., McClellan, W.J., Wendt, M.D., Wada, C., Frey, R., Hansen, T.M., Hubbard, R., Park, C.H., Li, L., Magoc, T.J., Albert, D.H., Lin, X., Warder, S.E., Kovar, P., Huang, X., Wilcox, D., Wang, R., Rajaraman, G., Petros, A.M., Hutchins, C.W., Panchal, S.C., Sun, C., Elmore, S.W., Shen, Y., Kati, W.M., McDaniel, K.F.

(2017) J Med Chem 60: 3828-3850

• PubMed: 28368119 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b00017
• Primary Citation of Related Structures:  
  5UEU, 5UEW, 5UEX, 5UEY, 5UEZ, 5UF0


• PubMed Abstract: 
  

Members of the BET family of bromodomain containing proteins have been identified as potential targets for blocking proliferation in a variety of cancer cell lines. A two-dimensional NMR fragment screen for binders to the bromodomains of BRD4 identified a phenylpyridazinone fragment with a weak binding affinity (1, K _i = 160 μM). SAR investigation of fragment 1, aided by X-ray structure-based design, enabled the synthesis of potent pyridone and macrocyclic pyridone inhibitors exhibiting single digit nanomolar potency in both biochemical and cell based assays. Advanced analogs in these series exhibited high oral exposures in rodent PK studies and demonstrated significant tumor growth inhibition efficacy in mouse flank xenograft models.

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Organizational Affiliation: 

AbbVie Inc. , 1 North Waukegan Road, North Chicago, Illinois 60064, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	109	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
89D	B [auth A]	17-{[ethyl(dihydroxy)-lambda~4~-sulfanyl]amino}-11,13-difluoro-2-methyl-6,7,8,9-tetrahydrodibenzo[4,5:7,8][1,6]dioxacyclododecino[3,2-c]pyridin-3(2H)-one C24 H26 F2 N2 O5 S VWDSFGMYIKNVLS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
89D	Binding MOAD:  5UEX	Ki: 1.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.279 
• R-Value Work: 0.236 
• R-Value Observed: 0.238 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.244	α = 90
b = 74.421	β = 90
c = 33.333	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
Coot	model building
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): Park, C.H.

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2017-05-24
  Changes: Database references