FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Protein-Protein Interaction Inhibition (2P2I)-Oriented Chemical Library Accelerates Hit Discovery.

Milhas, S.Raux, B.Betzi, S.Derviaux, C.Roche, P.Restouin, A.Basse, M.J.Rebuffet, E.Lugari, A.Badol, M.Kashyap, R.Lissitzky, J.C.Eydoux, C.Hamon, V.Gourdel, M.E.Combes, S.Zimmermann, P.Aurrand-Lions, M.Roux, T.Rogers, C.Muller, S.Knapp, S.Trinquet, E.Collette, Y.Guillemot, J.C.Morelli, X.

(2016) ACS Chem Biol 11: 2140-2148

  • DOI: https://doi.org/10.1021/acschembio.6b00286
  • Primary Citation of Related Structures:  
    5DLX, 5DLZ

  • PubMed Abstract: 

    Protein-protein interactions (PPIs) represent an enormous source of opportunity for therapeutic intervention. We and others have recently pinpointed key rules that will help in identifying the next generation of innovative drugs to tackle this challenging class of targets within the next decade. We used these rules to design an oriented chemical library corresponding to a set of diverse "PPI-like" modulators with cores identified as privileged structures in therapeutics. In this work, we purchased the resulting 1664 structurally diverse compounds and evaluated them on a series of representative protein-protein interfaces with distinct "druggability" potential using homogeneous time-resolved fluorescence (HTRF) technology. For certain PPI classes, analysis of the hit rates revealed up to 100 enrichment factors compared with nonoriented chemical libraries. This observation correlates with the predicted "druggability" of the targets. A specific focus on selectivity profiles, the three-dimensional (3D) molecular modes of action resolved by X-ray crystallography, and the biological activities of identified hits targeting the well-defined "druggable" bromodomains of the bromo and extraterminal (BET) family are presented as a proof-of-concept. Overall, our present study illustrates the potency of machine learning-based oriented chemical libraries to accelerate the identification of hits targeting PPIs. A generalization of this method to a larger set of compounds will accelerate the discovery of original and potent probes for this challenging class of targets.

  • Organizational Affiliation

    Goethe-University , Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Science, Campus Riedberg, Max-von Laue Str. 9, 60438 Frankfurt am Main, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4127Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5D1

Download Ideal Coordinates CCD File 
B [auth A]N-{[1-(3-methylbenzyl)piperidin-4-yl]methyl}-4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]butanamide
C28 H35 N3 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
5D1 Binding MOAD:  5DLZ Kd: 1800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.263α = 90
b = 44.236β = 90
c = 78.436γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection