6FQU

Crystal structure of CREBBP bromodomain complexd with DR09


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules.

Zhu, J.Dong, J.Batiste, L.Unzue, A.Dolbois, A.Pascanu, V.Sledz, P.Nevado, C.Caflisch, A.

(2018) ACS Med Chem Lett 9: 929-934

  • DOI: 10.1021/acsmedchemlett.8b00286
  • Primary Citation of Related Structures:  
    5MME, 5MMG, 5MPK, 5MPN, 6FQU, 6FQO, 6FR0, 6FRF, 5ENG, 5EP7, 5EIC, 5H85, 5OWK

  • PubMed Abstract: 
  • We analyze 20 crystal structures of complexes between the CBP bromodomain and small-molecule ligands that belong to eight different chemotypes identified by docking. The binding motif of the moiety that mimics the natural ligand (acetylated side chain of lysine) at the bottom of the binding pocket is conserved ...

    We analyze 20 crystal structures of complexes between the CBP bromodomain and small-molecule ligands that belong to eight different chemotypes identified by docking. The binding motif of the moiety that mimics the natural ligand (acetylated side chain of lysine) at the bottom of the binding pocket is conserved. In stark contrast, the rest of the ligands form different interactions with different side chains and backbone polar groups on the outer rim of the binding pocket. Hydrogen bonds are direct or water-bridged. van der Waals contacts are optimized by rotations of hydrophobic side chains and a slight inward displacement of the ZA loop. Rare types of interactions are observed for some of the ligands.


    Organizational Affiliation

    Department of Biochemistry, and Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CREB-binding proteinA119Homo sapiensMutation(s): 0 
Gene Names: CREBBPCBP
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens)
Explore Q92793 
Go to UniProtKB:  Q92793
PHAROS:  Q92793
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E3B (Subject of Investigation/LOI)
Query on E3B

Download Ideal Coordinates CCD File 
B [auth A]1-[3-[3-[3,3-bis(fluoranyl)piperidin-1-yl]phenyl]-4-ethoxy-phenyl]ethanone
C21 H23 F2 N O2
SEPRJZNGZUHEJW-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
E3B Binding MOAD:  6FQU IC50: 2200 (nM) from 1 assay(s)
BindingDB:  6FQU IC50: 2200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.258α = 90
b = 49.762β = 90
c = 80.576γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-02-14 
  • Released Date: 2018-08-29 
  • Deposition Author(s): Zhu, J., Caflisch, A.

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references