4Z1S | pdb_00004z1s

Crystal structure of the first bromodomain of human BRD4 with benzotriazolo-diazepine scaffold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 
    0.220 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Discovery of Benzotriazolo[4,3-d][1,4]diazepines as Orally Active Inhibitors of BET Bromodomains.

Taylor, A.M.Vaswani, R.G.Gehling, V.S.Hewitt, M.C.Leblanc, Y.Audia, J.E.Bellon, S.Cummings, R.T.Cote, A.Harmange, J.C.Jayaram, H.Joshi, S.Lora, J.M.Mertz, J.A.Neiss, A.Pardo, E.Nasveschuk, C.G.Poy, F.Sandy, P.Setser, J.W.Sims, R.J.Tang, Y.Albrecht, B.K.

(2016) ACS Med Chem Lett 7: 145-150

  • DOI: https://doi.org/10.1021/ml500411h
  • Primary Citation Related Structures: 
    4X2I, 4Z1Q, 4Z1S

  • PubMed Abstract: 

    Inhibition of the bromodomains of the BET family, of which BRD4 is a member, has been shown to decrease myc and interleukin (IL) 6 in vivo, markers that are of therapeutic relevance to cancer and inflammatory disease, respectively. Herein we report substituted benzo[b]isoxazolo[4,5-d]azepines and benzotriazolo[4,3-d][1,4]diazepines as fragment-derived novel inhibitors of the bromodomain of BRD4. Compounds from these series were potent and selective in cells, and subsequent optimization of microsomal stability yielded representatives that demonstrated dose- and time-dependent reduction of plasma IL-6 in mice.


  • Organizational Affiliation
    • Constellation Pharmaceuticals , 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States.

Macromolecule Content 

  • Total Structure Weight: 30.57 kDa 
  • Atom Count: 2,502 
  • Modeled Residue Count: 251 
  • Deposited Residue Count: 252 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4
A, B
126Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
559

Query on 559



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
5-[(4S)-6-(4-chlorophenyl)-1,4-dimethyl-5,6-dihydro-4H-[1,2,4]triazolo[4,3-a][1,5]benzodiazepin-8-yl]pyridin-2-amine
C23 H21 Cl N6
SBRJLPKKZHHGCO-AWEZNQCLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free:  0.220 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.376α = 82.6
b = 39.508β = 75.43
c = 57.358γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2026-03-04
    Changes: Refinement description, Structure summary