4TQN

Crystal structure of the bromodomain of human CREBBP in complex with UL04

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Discovery of CREBBP Bromodomain Inhibitors by High-Throughput Docking and Hit Optimization Guided by Molecular Dynamics.

Xu, M., Unzue, A., Dong, J., Spiliotopoulos, D., Nevado, C., Caflisch, A.

(2016) J Med Chem 59: 1340-1349

  • DOI: 10.1021/acs.jmedchem.5b00171
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • We have identified two chemotypes of CREBBP bromodomain ligands by fragment-based high-throughput docking. Only 17 molecules from the original library of two-million compounds were tested in vitro. Optimization of the two low-micromolar hits, the 4-a ...

    We have identified two chemotypes of CREBBP bromodomain ligands by fragment-based high-throughput docking. Only 17 molecules from the original library of two-million compounds were tested in vitro. Optimization of the two low-micromolar hits, the 4-acylpyrrole 1 and acylbenzene 9, was driven by molecular dynamics results which suggested improvement of the polar interactions with the Arg1173 side chain at the rim of the binding site. The synthesis of only two derivatives of 1 yielded the 4-acylpyrrole 6 which shows a single-digit micromolar affinity for the CREBBP bromodomain and a ligand efficiency of 0.34 kcal/mol per non-hydrogen atom. Optimization of the acylbenzene hit 9 resulted in a series of derivatives with nanomolar potencies, good ligand efficiency and selectivity (see Unzue, A.; Xu, M.; Dong, J.; Wiedmer, L.; Spiliotopoulos, D.; Caflisch, A.; Nevado, C.Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain. J. Med. Chem. 2015, DOI: 10.1021/acs.jmedchem.5b00172). The in silico predicted binding mode of the acylbenzene derivative 10 was validated by solving the structure of the complex with the CREBBP bromodomain.

    Organizational Affiliation: 

    Department of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057, Zürich, 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 (PDB Primary Data), 2.3.1 (UniProt)
Find proteins for Q92793 (Homo sapiens)
Go to UniProtKB:  Q92793
NIH Common Fund Data Resources
PHAROS  Q92793
GTEx  ENSG00000005339
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UL4
Query on UL4
Download CCD File 
A
3-[(5-acetyl-2-ethoxyphenyl)carbamoyl]benzoic acid
C18 H17 N O5
GFOBMGVVDGTGAJ-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UL4Kd:  670   nM  BindingDB
UL4Kd:  2000   nM  BindingDB
UL4IC50:  8700   nM  BindingDB
UL4Kd:  770   nM  Binding MOAD
UL4Kd:  770   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.938α = 90
b = 42.935β = 97.24
c = 51.983γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
XSCALEdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2014-06-11 
  • Released Date: 2015-06-24 
    • Deposition Author(s): Dong, J., Caflisch, A.

Revision History 

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references
  • Version 1.2: 2016-03-09
    Changes: Database references