4CVA | pdb_00004cva

MPS1 kinase with 3-aminopyridin-2-one inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4CVA/pdb

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


• Deposited: 2014-03-24 Released: 2015-04-08 
• Deposition Author(s): Fearon, D., Bavetsias, V., Bayliss, R., Schmitt, J., Westwood, I.M., vanMontfort, R.L.M., Jones, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.215 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Protein Kinase Selectivity of a 3-Aminopyridin-2- One Based Fragment Library, Identification of 3-Amino-5-(Pyridin-4-Yl)Pyridin-2(1H)-One as a Novel Scaffold for Mps1 Inhibition

Fearon, D., Bavetsias, V., Bayliss, R., Schmitt, J., Westwood, I.M., Van Montfort, R.L.M., Jones, K.

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: 36.85 kDa 
• Atom Count: 2,035 
• Modeled Residue Count: 255 
• 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  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WBI	B [auth A]	N-(6-oxo-1,6-dihydro-3,4'-bipyridin-5-yl)-4-(piperidin-1-yl)benzamide C22 H22 N4 O2 ABBVAIMDGQMDHS-UHFFFAOYSA-N
DMS	C [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
WBI	BindingDB:  4CVA	Ki: 2900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.215 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.46	α = 90
b = 107.16	β = 90
c = 112.75	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Fearon, D., Bavetsias, V., Bayliss, R., Schmitt, J., Westwood, I.M., vanMontfort, R.L.M., Jones, K.

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary