5C7N

Crystal structure of the human BRPF1 bromodomain in complex with Bromosporine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.2 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:  
    5C7N, 5C85, 5C87, 5DY7, 5DYA, 5DYC, 5E3D, 5E3G, 5EM3, 5EPR, 5EPS, 5EQ1, 5ETB, 5ETD, 5EV9, 5EVA, 5EWC, 5EWD, 5EWH

  • 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). Twenty crystal structures of BRPF1/ligand complexes show structural conservation in the acetyllysine binding site, common binding motifs, and unusual interactions (e ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PeregrinA116Homo sapiensMutation(s): 0 
Gene Names: BRPF1BR140
UniProt & NIH Common Fund Data Resources
Find proteins for P55201 (Homo sapiens)
Explore P55201 
Go to UniProtKB:  P55201
PHAROS:  P55201
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMF (Subject of Investigation/LOI)
Query on BMF

Download Ideal Coordinates CCD File 
B [auth A]Bromosporine
C17 H20 N6 O4 S
UYBRROMMFMPJAN-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download Ideal Coordinates CCD File 
C [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BMF Binding MOAD:  5C7N Kd: 270 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.502α = 90
b = 60.502β = 90
c = 63.111γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2015-06-24 
  • Released Date: 2015-07-08 
  • Deposition Author(s): Zhu, J., Caflisch, A.

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2016-06-22
    Changes: Database references