3VQU

CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 4-[(4-amino-5-cyano-6-ethoxypyridin-2- yl)amino]benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Diaminopyridine-based potent and selective mps1 kinase inhibitors binding to an unusual flipped-Peptide conformation.

Kusakabe, K.Ide, N.Daigo, Y.Itoh, T.Higashino, K.Okano, Y.Tadano, G.Tachibana, Y.Sato, Y.Inoue, M.Wada, T.Iguchi, M.Kanazawa, T.Ishioka, Y.Dohi, K.Tagashira, S.Kido, Y.Sakamoto, S.Yasuo, K.Maeda, M.Yamamoto, T.Higaki, M.Endoh, T.Ueda, K.Shiota, T.Murai, H.Nakamura, Y.

(2012) Acs Med.Chem.Lett. 3: 560-564

  • DOI: 10.1021/ml3000879

  • PubMed Abstract: 
  • Monopolar spindle 1 (Mps1) is an attractive cancer drug target due to the important role that it plays in centrosome duplication, the spindle assembly checkpoint, and the maintenance of chromosomal stability. A design based on JNK inhibitors with an ...

    Monopolar spindle 1 (Mps1) is an attractive cancer drug target due to the important role that it plays in centrosome duplication, the spindle assembly checkpoint, and the maintenance of chromosomal stability. A design based on JNK inhibitors with an aminopyridine scaffold and subsequent modifications identified diaminopyridine 9 with an IC50 of 37 nM. The X-ray structure of 9 revealed that the Cys604 carbonyl group of the hinge region flips to form a hydrogen bond with the aniline NH group in 9. Further optimization of 9 led to 12 with improved cellular activity, suitable pharmacokinetic profiles, and good in vivo efficacy in the mouse A549 xenograft model. Moreover, 12 displayed excellent selectivity over 95 kinases, indicating the contribution of its unusual flipped-peptide conformation to its selectivity.


    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.,Medicinal Research Laboratories, Drug Developmental Research Laboratories, and Innovative Drug Discovery Research Laboratories, Shionogi Pharmaceutical Research Center , 1-1 Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan.,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 ; Department of Medical Oncology, Shiga University of Medical Science , Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dual specificity protein kinase TTK
A
320Homo sapiensMutation(s): 0 
Gene Names: TTK (MPS1, MPS1L1)
EC: 2.7.12.1
Find proteins for P33981 (Homo sapiens)
Go to Gene View: TTK
Go to UniProtKB:  P33981
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
O22
Query on O22

Download SDF File 
Download CCD File 
A
4-[(4-amino-5-cyano-6-ethoxypyridin-2-yl)amino]benzamide
C15 H15 N5 O2
JUNWGTQNFTURHK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
O22IC50: 37 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.247 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.470α = 90.00
b = 106.070β = 90.00
c = 112.080γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
CrystalCleardata collection
SCALAdata scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Database references