6G0E

BRD4 (BD1) in complex with APSC-derived ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4127Homo 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
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EGN (Subject of Investigation/LOI)
Query on EGN

Download Ideal Coordinates CCD File 
B [auth A]4-[2-(4-cyclohexylpiperazin-4-ium-1-yl)-2-oxidanylidene-ethyl]sulfanyl-1-ethyl-quinolin-2-one
C23 H32 N3 O2 S
ZOILQSINXFCIAF-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.482α = 90
b = 46.749β = 90
c = 78.347γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
Cootmodel building

Structure Validation

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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
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description