6I8B

Crystal structure of Spindlin1 in complex with the inhibitor VinSpinIn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function.

Fagan, V.Johansson, C.Gileadi, C.Monteiro, O.Dunford, J.E.Nibhani, R.Philpott, M.Malzahn, J.Wells, G.Faram, R.Cribbs, A.P.Halidi, N.Li, F.Chau, I.Greschik, H.Velupillai, S.Allali-Hassani, A.Bennett, J.Christott, T.Giroud, C.Lewis, A.M.Huber, K.V.M.Athanasou, N.Bountra, C.Jung, M.Schule, R.Vedadi, M.Arrowsmith, C.Xiong, Y.Jin, J.Fedorov, O.Farnie, G.Brennan, P.E.Oppermann, U.

(2019) J Med Chem 62: 9008-9025

  • DOI: 10.1021/acs.jmedchem.9b00562
  • Primary Citation of Related Structures:  
    6I8B, 6I8Y, 6I8L

  • PubMed Abstract: 
  • Modifications of histone tails, including lysine/arginine methylation, provide the basis of a "chromatin or histone code". Proteins that contain "reader" domains can bind to these modifications and form specific effector complexes, which ultimately m ...

    Modifications of histone tails, including lysine/arginine methylation, provide the basis of a "chromatin or histone code". Proteins that contain "reader" domains can bind to these modifications and form specific effector complexes, which ultimately mediate chromatin function. The spindlin1 (SPIN1) protein contains three Tudor methyllysine/arginine reader domains and was identified as a putative oncogene and transcriptional coactivator. Here we report a SPIN1 chemical probe inhibitor with low nanomolar in vitro activity, exquisite selectivity on a panel of methyl reader and writer proteins, and with submicromolar cellular activity. X-ray crystallography showed that this Tudor domain chemical probe simultaneously engages Tudor domains 1 and 2 via a bidentate binding mode. Small molecule inhibition and siRNA knockdown of SPIN1, as well as chemoproteomic studies, identified genes which are transcriptionally regulated by SPIN1 in squamous cell carcinoma and suggest that SPIN1 may have a role in cancer related inflammation and/or cancer metastasis.


    Organizational Affiliation

    FRIAS-Freiburg Institute of Advanced Studies , University of Freiburg , 79104 Freiburg , Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spindlin-1BE222Homo sapiensMutation(s): 0 
Gene Names: SPIN1OCRSPIN
Find proteins for Q9Y657 (Homo sapiens)
Explore Q9Y657 
Go to UniProtKB:  Q9Y657
NIH Common Fund Data Resources
PHAROS  Q9Y657
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H7T
Query on H7T

Download CCD File 
B, E
2-[4-[2-[[2-[3-[2-azanyl-5-(cyclopropylmethoxy)-3,3-dimethyl-indol-6-yl]oxypropyl]-1,3-dihydroisoindol-5-yl]oxy]ethyl]-1,2,3-triazol-1-yl]-1-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]ethanone
C42 H58 N8 O4
XPEJZXWPKDAYFX-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
B, E
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
GLY
Query on GLY

Download CCD File 
B, E
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.875α = 90
b = 118.583β = 90
c = 43.808γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references