5JSG

Crystal structure of Spindlin1 bound to compound EML405


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Developing Spindlin1 small-molecule inhibitors by using protein microarrays

Bae, N.Viviano, M.Su, X.Lv, J.Cheng, D.Sagum, C.Castellano, S.Bai, X.Johnson, C.Khalil, M.I.Shen, J.Chen, K.Li, H.Sbardella, G.Bedford, M.T.

(2017) Nat. Chem. Biol. 13: 750-756

  • DOI: 10.1038/nchembio.2377
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The discovery of inhibitors of methyl- and acetyl-binding domains has provided evidence for the 'druggability' of epigenetic effector molecules. The small-molecule probe UNC1215 prevents methyl-dependent protein-protein interactions by engaging the a ...

    The discovery of inhibitors of methyl- and acetyl-binding domains has provided evidence for the 'druggability' of epigenetic effector molecules. The small-molecule probe UNC1215 prevents methyl-dependent protein-protein interactions by engaging the aromatic cage of MBT domains and, with lower affinity, Tudor domains. Using a library of tagged UNC1215 analogs, we screened a protein-domain microarray of human methyllysine effector molecules to rapidly detect compounds with new binding profiles with either increased or decreased specificity. Using this approach, we identified a compound (EML405) that acquired a novel interaction with the Tudor-domain-containing protein Spindlin1 (SPIN1). Structural studies facilitated the rational synthesis of SPIN1 inhibitors with increased selectivity (EML631-633), which engage SPIN1 in cells, block its ability to 'read' H3K4me3 marks and inhibit its transcriptional-coactivator activity. Protein microarrays can thus be used as a platform to 'target-hop' and identify small molecules that bind and compete with domain-motif interactions.


    Organizational Affiliation

    Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spindlin-1
A, B
222Homo sapiensMutation(s): 0 
Gene Names: SPIN1 (OCR, SPIN)
Find proteins for Q9Y657 (Homo sapiens)
Go to Gene View: SPIN1
Go to UniProtKB:  Q9Y657
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
6P9
Query on 6P9

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Download CCD File 
A, B
[2-(phenylamino)-1,4-phenylene]bis({4-[2-(pyrrolidin-1-yl)ethyl]piperidin-1-yl}methanone)
C36 H51 N5 O2
MJSAAVJPPGYWEY-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6P9Kd: 15000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.060α = 90.00
b = 123.908β = 92.30
c = 49.779γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data collection
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-05-08 
  • Released Date: 2017-05-10 
  • Deposition Author(s): Su, X., Li, H.

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references