6FO5

FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR #17

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

  • Deposited: 2018-02-06 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: 0.95 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A127Homo sapiensMutation(s): 0 
Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DZH
Query on DZH
Download Ideal Coordinates CCD File 
B [auth A]~{N}-[[4-[[7-ethyl-2,6-bis(oxidanylidene)purin-3-yl]methyl]phenyl]methyl]-2-oxidanylidene-1,3,4,5-tetrahydro-1-benzazepine-7-sulfonamide
C25 H26 N6 O5 S
GUZDPSZLHQZPSV-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DZH BindingDB:  6FO5 Kd: 190 (nM) from 1 assay(s)
IC50: min: 251, max: 283 (nM) from 2 assay(s)
Binding MOAD:  6FO5 Kd: 190 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.284α = 90
b = 47.498β = 90
c = 58.468γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-06 
  • 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  (Full details and data files)

  • 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