5FG5

Crystal structure of the bromodomain of human BRPF1 in complex with PFI-4 chemical probe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the bromodomain of human BRPF1 in complex with PFI-4 chemical probe

Tallant, C.Owen, D.R.Gerstenberger, B.S.Savitsky, P.Chaikuad, A.Fedorov, O.Nunez-Alonso, G.Filippakopoulos, P.von Delft, F.Arrowsmith, C.H.Edwards, A.M.Brennan, P.E.Bountra, C.Muller, S.Knapp, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peregrin
A, B
116Homo 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
GTEx:  ENSG00000156983 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55201
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5XF
Query on 5XF

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
~{N}-(1,3-dimethyl-2-oxidanylidene-6-pyrrolidin-1-yl-benzimidazol-5-yl)-2-methoxy-benzamide
C21 H24 N4 O3
QCIJLRJBZDBVDB-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
D [auth B]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5XF BindingDB:  5FG5 Kd: 13 (nM) from 1 assay(s)
IC50: min: 50, max: 172 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.919α = 90
b = 68.141β = 94.33
c = 72.656γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description