6I8Y | pdb_00006i8y

Crystal structure of Spindlin1 in complex with the Methyltransferase inhibitor A366

• PDB DOI: https://doi.org/10.2210/pdb6I8Y/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-21 Released: 2018-12-26 
• Deposition Author(s): Srikannathasan, V., Johansson, C., Gileadi, C., Shrestha, L., Sorrell, F.J., Krojer, T., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.C.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

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

• PubMed: 31550156 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b00562
• Primary Citation Related Structures: 
  6I8B, 6I8L, 6I8Y


• 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 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.

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Organizational Affiliation: 
• Structural Genomics Consortium, Nuffield Department of Medicine , University of Oxford , OX3 7DQ Oxford , U.K.
Target Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K.
Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, NIHR Bio-medical Research Centre , University of Oxford , Oxford OX3 7LD , U.K.
Structural Genomics Consortium , University of Toronto , 101 College Street , Toronto , Ontario M5G 1L7 , Canada.
Department of Urology, Center for Clinical Research, Medical Center, Signalling Research Centres BIOSS and CIBSS , University of Freiburg , D-79106 Freiburg , Germany.
FRIAS-Freiburg Institute of Advanced Studies , University of Freiburg , 79104 Freiburg , Germany.
Institute of Pharmaceutical Sciences , University of Freiburg , Albertstraße 25 , 79104 Freiburg , Germany.
Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences , Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States.
Alzheimer's Research UK Oxford Drug Discovery Institute, Nuffield Department of Medicine , University of Oxford , OX3 7FZ Oxford , U.K.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.59 kDa 
• Atom Count: 1,727 
• Modeled Residue Count: 190 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spindlin-1	A	222	Homo sapiens	Mutation(s): 0  Gene Names: SPIN1, OCR, SPIN
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y657 (Homo sapiens) Explore Q9Y657  Go to UniProtKB:  Q9Y657
PHAROS:  Q9Y657 GTEx:  ENSG00000106723

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2OD	B [auth A], C [auth A]	5'-methoxy-6'-[3-(pyrrolidin-1-yl)propoxy]spiro[cyclobutane-1,3'-indol]-2'-amine C19 H27 N3 O2 BKCDJTRMYWSXMC-UHFFFAOYSA-N
MPD	G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2OD	BindingDB:  6I8Y	Kd: min: 110, max: 393 (nM) from 3 assay(s)
		IC50: min: 72, max: 1500 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.17	α = 90
b = 116.17	β = 90
c = 43.63	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Srikannathasan, V., Johansson, C., Gileadi, C., Shrestha, L., Sorrell, F.J., Krojer, T., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.C.T.

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Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description