5ENH

Crystal structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with compound-12 N11528 (SGC - Diamond I04-1 fragment screening)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain.

Cox, O.B.Krojer, T.Collins, P.Monteiro, O.Talon, R.Bradley, A.Fedorov, O.Amin, J.Marsden, B.D.Spencer, J.von Delft, F.Brennan, P.E.

(2016) Chem Sci 7: 2322-2330

  • DOI: https://doi.org/10.1039/c5sc03115j
  • Primary Citation of Related Structures:  
    5ENB, 5ENC, 5ENE, 5ENF, 5ENH, 5ENI, 5ENJ

  • PubMed Abstract: 

    Research into the chemical biology of bromodomains has been driven by the development of acetyl-lysine mimetics. The ligands are typically anchored by binding to a highly conserved asparagine residue. Atypical bromodomains, for which the asparagine is mutated, have thus far proven elusive targets, including PHIP(2) whose parent protein, PHIP, has been linked to disease progression in diabetes and cancers. The PHIP(2) binding site contains a threonine in place of asparagine, and solution screening have yielded no convincing hits. We have overcome this hurdle by combining the sensitivity of X-ray crystallography, used as the primary fragment screen, with a strategy for rapid follow-up synthesis using a chemically-poised fragment library, which allows hits to be readily modified by parallel chemistry both peripherally and in the core. Our approach yielded the first reported hit compounds of PHIP(2) with measurable IC 50 values by an AlphaScreen competition assay. The follow-up libraries of four poised fragment hits improved potency into the sub-mM range while showing good ligand efficiency and detailed structural data.


  • Organizational Affiliation

    Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PH-interacting protein131Homo sapiensMutation(s): 0 
Gene Names: PHIPWDR11
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWQ0 (Homo sapiens)
Explore Q8WWQ0 
Go to UniProtKB:  Q8WWQ0
PHAROS:  Q8WWQ0
GTEx:  ENSG00000146247 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WWQ0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5QB
Query on 5QB

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[(2,6-dimethoxyphenyl)methyl]ethanamide
C11 H15 N O3
KOFRPILEEFGDBE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.84α = 90
b = 92.606β = 90
c = 24.06γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description