6DMJ

A multiconformer ligand model of inhibitor 53W bound to CREB binding protein bromodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 5CFW - determined by Chekler, E.L., Jones, L.H.  

Literature

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps.

van Zundert, G.Hudson, B.M.de Oliveira, S.Keedy, D.A.Fonseca, R.Heliou, A.Suresh, P.Borrelli, K.Day, T.Fraser, J.van den Bedem, H.

(2018) J. Med. Chem. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
A
127Homo sapiensMutation(s): 0 
Gene Names: BRD4 (HUNK1)
Find proteins for O60885 (Homo sapiens)
Go to Gene View: BRD4
Go to UniProtKB:  O60885
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
53W
Query on 53W

Download SDF File 
Download CCD File 
A
5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[2-(4-methoxyphenyl)ethyl]-1-[2-(morpholin-4-yl)ethyl]-1H-benzimidazole
C27 H32 N4 O3
RQFUKBAHMUVXDA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.610α = 90.00
b = 50.270β = 90.00
c = 57.210γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
BUSTERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release