6MO7 | pdb_00006mo7

N-terminal bromodomain of human BRD2 with N-((4-(3-(N-cyclopentylsulfamoyl)-4-methylphenyl)-3-methylisoxazol-5-yl)methyl)acetamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6MO7/pdb

• Classification: transcription/transcription inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-04 Released: 2019-01-23 
• Deposition Author(s): Lansdon, E.B., Newby, Z.E.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.230 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Structure-guided discovery of a novel, potent, and orally bioavailable 3,5-dimethylisoxazole aryl-benzimidazole BET bromodomain inhibitor.

Sperandio, D., Aktoudianakis, V., Babaoglu, K., Chen, X., Elbel, K., Chin, G., Corkey, B., Du, J., Jiang, B., Kobayashi, T., Mackman, R., Martinez, R., Yang, H., Zablocki, J., Kusam, S., Jordan, K., Webb, H., Bates, J.G., Lad, L., Mish, M., Niedziela-Majka, A., Metobo, S., Sapre, A., Hung, M., Jin, D., Fung, W., Kan, E., Eisenberg, G., Larson, N., Newby, Z.E.R., Lansdon, E., Tay, C., Neve, R.M., Shevick, S.L., Breckenridge, D.G.

(2019) Bioorg Med Chem 27: 457-469

• PubMed: 30606676 
• DOI: https://doi.org/10.1016/j.bmc.2018.11.020
• Primary Citation Related Structures: 
  6MO7, 6MO8, 6MO9, 6MOA


• PubMed Abstract: 
  

  The bromodomain and extra-terminal (BET) family of proteins, consisting of the bromodomains containing protein 2 (BRD2), BRD3, BRD4, and the testis-specific BRDT, are key epigenetic regulators of gene transcription and has emerged as an attractive target for anticancer therapy. Herein, we describe the discovery of a novel potent BET bromodomain inhibitor, using a systematic structure-based approach focused on improving potency, metabolic stability, and permeability. The optimized dimethylisoxazole aryl-benzimidazole inhibitor exhibited high potency towards BRD4 and related BET proteins in biochemical and cell-based assays and inhibited tumor growth in two proof-of-concept preclinical animal models.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA. Electronic address: [e-mail].
Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.
Department of Structural Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.
Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.
Department of Drug Metabolism, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.92 kDa 
• Atom Count: 3,158 
• Modeled Residue Count: 327 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B, C	126	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
JWA	D [auth A], E [auth B], F [auth C]	N-({4-[3-(cyclopentylsulfamoyl)-4-methylphenyl]-3-methyl-1,2-oxazol-5-yl}methyl)acetamide C19 H25 N3 O4 S WUVRAMLGTYQHNJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.230 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.058	α = 90
b = 55.833	β = 95.24
c = 68.467	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Lansdon, E.B., Newby, Z.E.R.

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Database references
• Version 1.2: 2024-03-13
  Changes: Advisory, Data collection, Database references