4CV9 | pdb_00004cv9

MPS1 kinase with 3-aminopyridin-2-one inhibitors

PDB DOI: https://doi.org/10.2210/pdb4CV9/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.232 (Depositor), 0.248 (DCC)
R-Value Work:
0.185 (Depositor), 0.203 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 36.97 kDa
Atom Count: 2,027
Modeled Residue Count: 255
Deposited Residue Count: 313
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33981
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W2K Query on W2K Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-(4-Methylpiperazin-1-yl)-N-(2-oxo-5-(pyridin-4-yl)-1,2-dihydropyridin-3-yl)benzamide C₂₂ H₂₃ N₅ O₂ GPWFEKSGAWXQOP-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
W2K	BindingDB: 4CV9	Ki: 4800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.232 (Depositor), 0.248 (DCC)
R-Value Work: 0.185 (Depositor), 0.203 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.38	α = 90
b = 108.72	β = 90
c = 113.56	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-04-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-04-08
Type: Initial release
Version 1.1: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary