Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.53 kDa 
• Atom Count: 1325 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

5M3A

Crystal structure of BRD4 BROMODOMAIN 1 IN COMPLEX WITH LIGAND 2

• PDB DOI: 10.2210/pdb5M3A/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2016-10-14 Released: 2017-09-27 
• Deposition Author(s): Kessler, D., Mayer, M., Engelhardt, H., Wolkerstorfer, B., Geist, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.214 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Literature

Direct NMR Probing of Hydration Shells of Protein Ligand Interfaces and Its Application to Drug Design.

Geist, L., Mayer, M., Cockcroft, X.L., Wolkerstorfer, B., Kessler, D., Engelhardt, H., McConnell, D.B., Konrat, R.

(2017) J Med Chem 60: 8708-8715

• PubMed: 28910100 
• DOI: 10.1021/acs.jmedchem.7b00845
• Primary Citation of Related Structures:  
  5M39, 5M3A


• PubMed Abstract: 
  

Fragment-based drug design exploits initial screening of low molecular weight compounds and their concomitant affinity improvement. The multitude of possible chemical modifications highlights the necessity to obtain structural information about the binding mode of a fragment. Herein we describe a novel NMR methodology (LOGSY titration) that allows the determination of binding modes of low affinity binders in the protein-ligand interface and reveals suitable ligand positions for the addition of functional groups that either address or substitute protein-bound water, information of utmost importance for drug design. The particular benefit of the methodology and in contrast to conventional ligand-based methods is the independence of the molecular weight of the protein under study. The validity of the novel approach is demonstrated on two ligands interacting with bromodomain 1 of bromodomain containing protein 4, a prominent cancer target in pharmaceutical industry.

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Organizational Affiliation: 

Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, University of Vienna , Campus Vienna Biocenter 5, A-1030 Vienna, Austria.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7E7	D [auth A]	3-methyl-6-(1-methyl-5-phenoxy-pyrazol-4-yl)-[1,2,4]triazolo[4,3-b]pyridazine C16 H14 N6 O PABNTFSOLMJZLZ-UHFFFAOYSA-N
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7E7	BindingDB:  5M3A	IC50: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.214 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.26	α = 90
b = 44.18	β = 90
c = 78.49	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-10-14 
• Released Date: 2017-09-27 
Deposition Author(s): Kessler, D., Mayer, M., Engelhardt, H., Wolkerstorfer, B., Geist, L.

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references