5EHO

Rapid Discovery of Pyrido[3,4-d]pyrimidine Inhibitors of Monopolar Spindle kinase 1 (MPS1) Using a Structure-Based Hydridization Approach

• PDB DOI: https://doi.org/10.2210/pdb5EHO/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-28 Released: 2016-11-09 
• Deposition Author(s): Innocenti, P., Woodward, H.L., Solanki, S., Naud, N., Westwood, I.M., Cronin, N., Hayes, A., Roberts, J., Henley, A.T., Baker, R., Faisal, A., Mak, G., Box, G., Valenti, M., De Haven Brandon, A., O'Fee, L., Saville, J., Schmitt, J., Burke, R., van Montfort, R.L.M., Raymaud, F.I., Eccles, S.A., Linardopoulos, S., Blagg, J., Hoelder, S.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.207 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Literature

Rapid Discovery of Pyrido[3,4-d]pyrimidine Inhibitors of Monopolar Spindle kinase 1 (MPS1) Using a Structure-Based Hydridization Approach

Innocenti, P., Woodward, H.L., Solanki, S., Naud, N., Westwood, I.M., Cronin, N., Hayes, A., Roberts, J., Henley, A.T., Baker, R., Faisal, A., Mak, G., Box, G., Valenti, M., De Haven Brandon, A., O'Fee, L., Saville, J., Schmitt, J., Burke, R., van Montfort, R.L.M., Raymaud, F.I., Eccles, S.A., Linardopoulos, S., Blagg, J., Hoelder, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.62 kDa 
• Atom Count: 2,124 
• Modelled Residue Count: 258 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase TTK	A	313	Homo sapiens	Mutation(s): 0  Gene Names: TTK, MPS1, MPS1L1 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P33981 (Homo sapiens) Explore P33981  Go to UniProtKB:  P33981
PHAROS:  P33981 GTEx:  ENSG00000112742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5O1	B [auth A]	~{N}8-cyclohexyl-~{N}2-[2-methoxy-4-(1-methylpyrazol-4-yl)phenyl]pyrido[3,4-d]pyrimidine-2,8-diamine C24 H27 N7 O DIBCUQSRSKMAFL-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5O1	BindingDB:  5EHO	Ki: 1.3 (nM) from 1 assay(s)
		IC50: min: 9, max: 220 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.207 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.945	α = 90
b = 105.486	β = 90
c = 111.692	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Innocenti, P., Woodward, H.L., Solanki, S., Naud, N., Westwood, I.M., Cronin, N., Hayes, A., Roberts, J., Henley, A.T., Baker, R., Faisal, A., Mak, G., Box, G., Valenti, M., De Haven Brandon, A., O'Fee, L., Saville, J., Schmitt, J., Burke, R., van Montfort, R.L.M., Raymaud, F.I., Eccles, S.A., Linardopoulos, S., Blagg, J., Hoelder, S.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	--

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence
• Version 1.2: 2018-04-04
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references