4C66 | pdb_00004c66

Discovery of Epigenetic Regulator I-BET762: Lead Optimization to Afford a Clinical Candidate Inhibitor of the BET Bromodomains

• PDB DOI: https://doi.org/10.2210/pdb4C66/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-09-17 Released: 2013-10-02 
• Deposition Author(s): Chung, C., Mirguet, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.266 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Discovery of Epigenetic Regulator I-Bet762: Lead Optimization to Afford a Clinical Candidate Inhibitor of the Bet Bromodomains.

Mirguet, O., Gosmini, R., Toum, J., Clement, C., Barnathan, M., Brusq, J., Mordaunt, J.E., Grimes, R., Crowe, M., Pineau, O., Ajakane, M., Daugan, A., Jeffrey, P., Cutler, L., Haynes, A., Smithers, N., Chung, C., Bamborough, P., Uings, I.J., Lewis, T., Witherington, J., Parr, N., Prinjha, R., Nicodeme, E.

(2013) J Med Chem 56: 7501

• PubMed: 24015967 
• DOI: https://doi.org/10.1021/jm401088k
• Primary Citation Related Structures: 
  4C66, 4C67


• PubMed Abstract: 
  

  The bromo and extra C-terminal domain (BET) family of bromodomains are involved in binding epigenetic marks on histone proteins, more specifically acetylated lysine residues. This paper describes the discovery and structure-activity relationships (SAR) of potent benzodiazepine inhibitors that disrupt the function of the BET family of bromodomains (BRD2, BRD3, and BRD4). This work has yielded a potent, selective compound I-BET762 that is now under evaluation in a phase I/II clinical trial for nuclear protein in testis (NUT) midline carcinoma and other cancers.

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Organizational Affiliation: 
• Centre de Recherches François Hyafil, GlaxoSmithKline R&D , 25 Avenue du Québec, 91140 Villebon-sur-Yvette, France.

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: 15.31 kDa 
• Atom Count: 1,190 
• Modeled Residue Count: 126 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BROMODOMAIN-CONTAINING PROTEIN 4	A	126	Homo sapiens	Mutation(s): 0
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
H4C	B [auth A]	4-(2-chlorophenyl)-2-ethyl-9-methyl-6,8-dihydrothieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-10-ium C17 H16 Cl N4 S VMZUTJCNQWMAGF-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.266 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.464	α = 90
b = 44.664	β = 90
c = 78.664	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Chung, C., Mirguet, O.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2013-10-30
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other