5XPI

Structure of UHRF1 TTD in complex with NV01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of Small-Molecule Antagonists of the H3K9me3 Binding to UHRF1 Tandem Tudor Domain

Senisterra, G.Zhu, H.Y.Luo, X.Zhang, H.Xun, G.Lu, C.Xiao, W.Hajian, T.Loppnau, P.Chau, I.Li, F.Allali-Hassani, A.Atadja, P.Oyang, C.Li, E.Brown, P.J.Arrowsmith, C.H.Zhao, K.Yu, Z.Vedadi, M.

(2018) SLAS Discov 23: 930-940

  • DOI: https://doi.org/10.1177/2472555218766278
  • Primary Citation of Related Structures:  
    5XPI

  • PubMed Abstract: 

    Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is a multidomain protein that plays a critical role in maintaining DNA methylation patterns through concurrent recognition of hemimethylated DNA and histone marks by various domains, and recruitment of DNA methyltransferase 1 (DNMT1). UHRF1 is overexpressed in various cancers, including breast cancer. The tandem tudor domain (TTD) of UHRF1 specifically and tightly binds to histone H3 di- or trimethylated at lysine 9 (H3K9me2 or H3K9me3, respectively), and this binding is essential for UHRF1 function. We developed an H3K9me3 peptide displacement assay, which was used to screen a library of 44,000 compounds for small molecules that disrupt the UHRF1-H3K9me3 interaction. This screen resulted in the identification of NV01, which bound to UHRF1-TTD with a K d value of 5 μM. The structure of UHRF1-TTD in complex with NV01 confirmed binding to the H3K9me3-binding pocket. Limited structure-based optimization of NV01 led to the discovery of NV03 (K d of 2.4 μM). These well-characterized small-molecule antagonists of the UHRF1-H3K9me2/3 interaction could be valuable starting chemical matter for developing more potent and cell-active probes toward further characterizing UHRF1 function, with possible applications as anticancer therapeutics.


  • Organizational Affiliation

    1 Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UHRF1157Homo sapiensMutation(s): 0 
Gene Names: UHRF1ICBP90NP95RNF106
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T88 (Homo sapiens)
Explore Q96T88 
Go to UniProtKB:  Q96T88
PHAROS:  Q96T88
GTEx:  ENSG00000276043 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96T88
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8C3
Query on 8C3

Download Ideal Coordinates CCD File 
B [auth A]N-[3-(diethylamino)propyl]-2-(12-methyl-9-oxidanylidene-5-thia-1,10,11-triazatricyclo[6.4.0.0^2,6]dodeca-2(6),3,7,11-tetraen-10-yl)ethanamide
C18 H25 N5 O2 S
DRDIHUMOFDGYRJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.001α = 90
b = 99.001β = 90
c = 41.315γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection
  • Version 1.2: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description