5ENG

Crystal structure of the bromodomain of human CREBBP in complex with UP39


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


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:  

  • 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 chai ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CREB-binding protein
A
119Homo sapiensMutation(s): 0 
Gene Names: CREBBP (CBP)
EC: 2.3.1.48
Find proteins for Q92793 (Homo sapiens)
Go to Gene View: CREBBP
Go to UniProtKB:  Q92793
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5QN
Query on 5QN

Download SDF File 
Download CCD File 
A
methyl 2-[2-(3,5-dihydro-2~{H}-pyrazin-4-yl)ethoxy]-5-[(5-ethanoyl-2-ethoxy-phenyl)carbamoyl]benzoate
C25 H29 N3 O6
HFLCQGIXUOKAGP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.237α = 90.00
b = 49.710β = 90.00
c = 80.346γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALAdata scaling
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-11-09 
  • Released Date: 2016-11-23 
  • Deposition Author(s): Dong, J., Caflisch, A.

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2018-10-10
    Type: Data collection, Database references