6G0D

BRD4 (BD1) in complex with APSC-derived ligands (e.g. LY294002)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of an Unexpected Similarity in Ligand Binding Between BRD4 and PPARgamma

Humbeck, L.Pretzel, J.Spitzer, S.Koch, O.

(2019) Chemrxiv 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A127Homo sapiensMutation(s): 1 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LY2 (Subject of Investigation/LOI)
Query on LY2

Download Ideal Coordinates CCD File 
C [auth A]2-MORPHOLIN-4-YL-7-PHENYL-4H-CHROMEN-4-ONE
C19 H17 N O3
CZQHHVNHHHRRDU-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LY2 BindingDB:  6G0D IC50: min: 5330, max: 1.24e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.295α = 90
b = 42.868β = 90
c = 79.582γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySPP 1736
German Federal Ministry for Education and Research (BMBF)GermanyBMBF Grant 1316053

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-08
    Type: Initial release