5C87

Crystal structure of the human BRPF1 bromodomain in complex with SEED2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Twenty Crystal Structures of Bromodomain and PHD Finger Containing Protein 1 (BRPF1)/Ligand Complexes Reveal Conserved Binding Motifs and Rare Interactions.

Zhu, J.Caflisch, A.

(2016) J.Med.Chem. 59: 5555-5561

  • DOI: 10.1021/acs.jmedchem.6b00215
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • BRPF1 plays a scaffolding role in transcription. We report on fragment screening by high-throughput docking to the BRPF1 bromodomain which resulted in six chemotypes with very favorable ligand efficiency (0.45-0.50 kcal/mol per non-hydrogen atom). Tw ...

    BRPF1 plays a scaffolding role in transcription. We report on fragment screening by high-throughput docking to the BRPF1 bromodomain which resulted in six chemotypes with very favorable ligand efficiency (0.45-0.50 kcal/mol per non-hydrogen atom). Twenty crystal structures of BRPF1/ligand complexes show structural conservation in the acetyllysine binding site, common binding motifs, and unusual interactions (e.g., the replacement of a conserved water molecule). The structural information is useful for the design of chemical probes.


    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
Peregrin
A
116Homo sapiensGene Names: BRPF1 (BR140)
Find proteins for P55201 (Homo sapiens)
Go to Gene View: BRPF1
Go to UniProtKB:  P55201
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
4YS
Query on 4YS

Download SDF File 
Download CCD File 
A
isoquinolin-1(2H)-one
C9 H7 N O
VDBNYAPERZTOOF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.182 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.559α = 90.00
b = 60.559β = 90.00
c = 63.599γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-06-25 
  • Released Date: 2016-05-25 
  • Deposition Author(s): Zhu, J., Caflisch, A.

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references