4Z93

BRD4 bromodomain 2 in complex with gamma-carboline-containing compound, number 18.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-Based Design of gamma-Carboline Analogues as Potent and Specific BET Bromodomain Inhibitors.

Ran, X.Zhao, Y.Liu, L.Bai, L.Yang, C.Y.Zhou, B.Meagher, J.L.Chinnaswamy, K.Stuckey, J.A.Wang, S.

(2015) J.Med.Chem. 58: 4927-4939

  • DOI: 10.1021/acs.jmedchem.5b00613

  • PubMed Abstract: 
  • Small-molecule inhibitors of bromodomain and extra terminal proteins (BET), including BRD2, BRD3, and BRD4 proteins have therapeutic potential for the treatment of human cancers and other diseases and conditions. In this paper, we report the design, ...

    Small-molecule inhibitors of bromodomain and extra terminal proteins (BET), including BRD2, BRD3, and BRD4 proteins have therapeutic potential for the treatment of human cancers and other diseases and conditions. In this paper, we report the design, synthesis, and evaluation of γ-carboline-containing compounds as a new class of small-molecule BET inhibitors. The most potent inhibitor (compound 18, RX-37) obtained from this study binds to BET bromodomain proteins (BRD2, BRD3, and BRD4) with Ki values of 3.2-24.7 nM and demonstrates high selectivity over other non-BET bromodomain-containing proteins. Compound 18 potently and selectively inhibits cell growth in human acute leukemia cell lines harboring the rearranged mixed lineage leukemia 1 gene. We have determined a cocrystal structure of 18 in complex with BRD4 BD2 at 1.4 Å resolution, which provides a solid structural basis for the compound's high binding affinity and for its further structure-based optimization. Compound 18 represents a promising lead compound for the development of a new class of therapeutics for the treatment of human cancer and other conditions.


    Organizational Affiliation

    †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
A
112Homo sapiensMutation(s): 0 
Gene Names: BRD4 (HUNK1)
Find proteins for O60885 (Homo sapiens)
Go to Gene View: BRD4
Go to UniProtKB:  O60885
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4LD
Query on 4LD

Download SDF File 
Download CCD File 
A
1-(3-cyclopropyl-5-methyl-1H-pyrazol-4-yl)-7-(3,5-dimethyl-1,2-oxazol-4-yl)-8-methoxy-5H-pyrido[4,3-b]indole
C24 H23 N5 O2
WHDUHJYPRJXLGF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4LDKd: 45 - 47 nM (100) BINDINGDB
4LDKi: 12 - 25 nM (100) BINDINGDB
4LDIC50: 37 - 76 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.862α = 90.00
b = 72.696β = 90.00
c = 32.115γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-08
    Type: Experimental preparation, Structure summary