4UP5

Crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and a chemical fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Competitive Binding of a Benzimidazole to the Histone-Binding Pocket of the Pygo Phd Finger.

Miller, T.C.R.Rutherford, T.J.Birchall, K.Chugh, J.Fiedler, M.Bienz, M.

(2014) ACS Chem Biol 9: 2864

  • DOI: 10.1021/cb500585s
  • Primary Citation of Related Structures:  
    4UP0, 4UP5

  • PubMed Abstract: 
  • The Pygo-BCL9 complex is a chromatin reader, facilitating β-catenin-mediated oncogenesis, and is thus emerging as a potential therapeutic target for cancer. Its function relies on two ligand-binding surfaces of Pygo's PHD finger that anchor the histone H3 tail methylated at lysine 4 (H3K4me) with assistance from the BCL9 HD1 domain ...

    The Pygo-BCL9 complex is a chromatin reader, facilitating β-catenin-mediated oncogenesis, and is thus emerging as a potential therapeutic target for cancer. Its function relies on two ligand-binding surfaces of Pygo's PHD finger that anchor the histone H3 tail methylated at lysine 4 (H3K4me) with assistance from the BCL9 HD1 domain. Here, we report the first use of fragment-based screening by NMR to identify small molecules that block protein-protein interactions by a PHD finger. This led to the discovery of a set of benzothiazoles that bind to a cleft emanating from the PHD-HD1 interface, as defined by X-ray crystallography. Furthermore, we discovered a benzimidazole that docks into the H3K4me specificity pocket and displaces the native H3K4me peptide from the PHD finger. Our study demonstrates the ligandability of the Pygo-BCL9 complex and uncovers a privileged scaffold as a template for future development of lead inhibitors of oncogenesis.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEINA99Homo sapiensMutation(s): 0 
Gene Names: BCL9LDLNB11PYGO2PP7910
UniProt & NIH Common Fund Data Resources
Find proteins for Q86UU0 (Homo sapiens)
Explore Q86UU0 
Go to UniProtKB:  Q86UU0
PHAROS:  Q86UU0
Find proteins for Q9BRQ0 (Homo sapiens)
Explore Q9BRQ0 
Go to UniProtKB:  Q9BRQ0
PHAROS:  Q9BRQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ86UU0Q9BRQ0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
94W
Query on 94W

Download Ideal Coordinates CCD File 
D [auth A]6-methoxy-1,3-benzothiazol-2-amine
C8 H8 N2 O S
KZHGPDSVHSDCMX-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
94W Binding MOAD:  4UP5 Kd: 2.50e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.27α = 90
b = 54.27β = 90
c = 57.655γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references