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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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

Kusakabe, K.I.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 

  • 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 ...

    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.


    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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity protein kinase TTKA321Homo sapiensMutation(s): 0 
Gene Names: TTKMPS1MPS1L1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O17 (Subject of Investigation/LOI)
Query on O17

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
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 = 70.587α = 90
b = 106.403β = 90
c = 114.318γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description