Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.4 kDa 
• Atom Count: 2,011 
• Modelled Residue Count: 258 
• Deposited Residue Count: 321 
• Unique protein chains: 1

 3WYY

CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH (E)-3-(4-((6-(((3s,5s,7s)-adamantan-1-yl)amino)-4-amino-5-cyanopyridin-2-yl)amino)-2-(cyanomethoxy)phenyl)-N-(2-methoxyethyl)acrylamide

• PDB DOI: 10.2210/pdb3WYY/pdb

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


• Deposited: 2014-09-10 Released: 2015-04-08 
• Deposition Author(s): Kusakabe, K., Ide, N., Daigo, Y., Itoh, T., Yamamoto, T., Kojima, E., Mitsuoka, Y., Tadano, G., Tagashira, S., Higashino, K., Okano, Y., Sato, Y., Inoue, M., Iguchi, M., Kanazawa, T., Ishioka, Y., Dohi, K., Kido, Y., Sakamoto, S., Ando, S., Maeda, M., Higaki, M., Yoshizawa, H., Murai, H., Nakamura, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.281 
• R-Value Work: 0.223 
• R-Value Observed: 0.229 

Literature

A unique hinge binder of extremely selective aminopyridine-based Mps1 (TTK) kinase inhibitors with cellular activity.

Kusakabe, K., Ide, N., Daigo, Y., Itoh, T., Yamamoto, T., Kojima, E., Mitsuoka, Y., Tadano, G., Tagashira, S., Higashino, K., Okano, Y., Sato, Y., Inoue, M., Iguchi, M., Kanazawa, T., Ishioka, Y., Dohi, K., Kido, Y., Sakamoto, S., Ando, S., Maeda, M., Higaki, M., Yoshizawa, H., Murai, H., Nakamura, Y.

(2015) Bioorg Med Chem 23: 2247-2260

• PubMed: 25801152 
• DOI: 10.1016/j.bmc.2015.02.042
• Primary Citation of Related Structures:  
  3WYX, 3WYY


• PubMed Abstract: 
  

Mps1, also known as TTK, is a dual-specificity kinase that regulates the spindle assembly check point. Increased expression levels of Mps1 are observed in cancer cells, and the expression levels correlate well with tumor grade. Such evidence points to selective inhibition of Mps1 as an attractive strategy for cancer therapeutics. Starting from an aminopyridine-based lead 3a that binds to a flipped-peptide conformation at the hinge region in Mps1, elaboration of the aminopyridine scaffold at the 2- and 6-positions led to the discovery of 19c that exhibited no significant inhibition for 287 kinases as well as improved cellular Mps1 and antiproliferative activities in A549 lung carcinoma cells (cellular Mps1 IC₅₀=5.3 nM, A549 IC₅₀=26 nM). A clear correlation between cellular Mps1 and antiproliferative IC₅₀ values indicated that the antiproliferative activity observed in A549 cells would be responsible for the cellular inhibition of Mps1. The X-ray structure of 19c in complex with Mps1 revealed that this compound retains the ability to bind to the peptide flip conformation. Finally, comparative analysis of the X-ray structures of 19c, a deamino analogue 33, and a known Mps1 inhibitor bound to Mps1 provided insights into the unique binding mode at the hinge region.

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Organizational Affiliation: 

Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase TTK	A	321	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O17	B [auth A]	(2E)-3-[4-({4-amino-5-cyano-6-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylamino]pyridin-2-yl}amino)-2-(cyanomethoxy)phenyl]-N-(2-methoxyethyl)prop-2-enamide C30 H35 N7 O3 XFGLTLTUEITKOH-SWLKYIRASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.281 
• R-Value Work: 0.223 
• R-Value Observed: 0.229 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.587	α = 90
b = 106.403	β = 90
c = 114.318	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Kusakabe, K., Ide, N., Daigo, Y., Itoh, T., Yamamoto, T., Kojima, E., Mitsuoka, Y., Tadano, G., Tagashira, S., Higashino, K., Okano, Y., Sato, Y., Inoue, M., Iguchi, M., Kanazawa, T., Ishioka, Y., Dohi, K., Kido, Y., Sakamoto, S., Ando, S., Maeda, M., Higaki, M., Yoshizawa, H., Murai, H., Nakamura, Y.

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2022-08-24
  Changes: Database references, Derived calculations