6FNX

FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR F1

  • Classification: DNA BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21
  • Mutation(s): No 

  • Deposited: 2018-02-05 Released: 2018-06-20 
  • Deposition Author(s): Raux, B., Betzi, S.
  • Funding Organization(s): Canceropole PACA Institut National du Cancer Conseil Regional PACA, Fondation FRM pour la Recherche Medicale, Agence Nationale de la Recherche ANR, Integrated Structural Biology (FRISBI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Integrated Strategy for Lead Optimization Based on Fragment Growing: The Diversity-Oriented-Target-Focused-Synthesis Approach.

Hoffer, L.Voitovich, Y.V.Raux, B.Carrasco, K.Muller, C.Fedorov, A.Y.Derviaux, C.Amouric, A.Betzi, S.Horvath, D.Varnek, A.Collette, Y.Combes, S.Roche, P.Morelli, X.

(2018) J Med Chem 61: 5719-5732

  • DOI: 10.1021/acs.jmedchem.8b00653
  • Primary Citation of Related Structures:  
    6FNX, 6FO5

  • PubMed Abstract: 
  • Over the past few decades, hit identification has been greatly facilitated by advances in high-throughput and fragment-based screenings. One major hurdle remaining in drug discovery is process automation of hit-to-lead (H2L) optimization. Here, we re ...

    Over the past few decades, hit identification has been greatly facilitated by advances in high-throughput and fragment-based screenings. One major hurdle remaining in drug discovery is process automation of hit-to-lead (H2L) optimization. Here, we report a time- and cost-efficient integrated strategy for H2L optimization as well as a partially automated design of potent chemical probes consisting of a focused-chemical-library design and virtual screening coupled with robotic diversity-oriented de novo synthesis and automated in vitro evaluation. The virtual library is generated by combining an activated fragment, corresponding to the substructure binding to the target, with a collection of functionalized building blocks using in silico encoded chemical reactions carefully chosen from a list of one-step organic transformations relevant in medicinal chemistry. The proof of concept was demonstrated using the optimization of bromodomain inhibitors as a test case, leading to the validation of several compounds with improved affinity by several orders of magnitude.


    Organizational Affiliation

    IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A127Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DYZ
Query on DYZ

Download CCD File 
A
7-ethyl-3-(phenylmethyl)purine-2,6-dione
C14 H14 N4 O2
XEPOHOPPWDSWQR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DYZIC50:  10   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.863α = 90
b = 44.175β = 90
c = 78.156γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-05 
  • Released Date: 2018-06-20 
  • Deposition Author(s): Raux, B., Betzi, S.

Funding OrganizationLocationGrant Number
Canceropole PACA Institut National du Cancer Conseil Regional PACAFrance--
Fondation FRM pour la Recherche MedicaleFrance--
Agence Nationale de la Recherche ANRFranceANR-15-CE18-0023
Integrated Structural Biology (FRISBI)FranceANR-10-INSB-05-01

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-25
    Changes: Data collection, Database references