Crystal structure of CREBBP bromodomain complexed with DK19

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.188 

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

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CREB-binding protein
A, B
119Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens)
Explore Q92793 
Go to UniProtKB:  Q92793
GTEx:  ENSG00000005339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92793
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0BC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C21 H18 N6 O3 S
Binding Affinity Annotations 
IDSourceBinding Affinity
0BC BindingDB:  5MPK Kd: 3 (nM) from 1 assay(s)
IC50: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.077α = 90
b = 60.204β = 90
c = 87.636γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-10
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references