6P5M | pdb_00006p5m

Discovery of a Novel, Highly Potent, and Selective Thieno[3,2-d]pyrimidinone-Based Cdc7 inhibitor with a Quinuclidine Moiety (TAK-931) as an Orally Active Investigational Anti-Tumor Agent


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.225 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of a Novel, Highly Potent, and Selective Thieno[3,2-d]pyrimidinone-Based Cdc7 Inhibitor with a Quinuclidine Moiety (TAK-931) as an Orally Active Investigational Antitumor Agent.

Kurasawa, O.Miyazaki, T.Homma, M.Oguro, Y.Imada, T.Uchiyama, N.Iwai, K.Yamamoto, Y.Ohori, M.Hara, H.Sugimoto, H.Iwata, K.Skene, R.Hoffman, I.Ohashi, A.Nomura, T.Cho, N.

(2020) J Med Chem 63: 1084-1104

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01427
  • Primary Citation Related Structures: 
    6P5M, 6P5P

  • PubMed Abstract: 

    In our pursuit of developing a novel, potent, and selective cell division cycle 7 (Cdc7) inhibitor, we optimized the previously reported thieno[3,2- d ]pyrimidinone analogue I showing time-dependent Cdc7 kinase inhibition and slow dissociation kinetics. These medicinal chemistry efforts led to the identification of compound 3d , which exhibited potent cellular activity, excellent kinase selectivity, and antitumor efficacy in a COLO205 xenograft mouse model. However, the issue of formaldehyde adduct formation emerged during a detailed study of 3d , which was deemed an obstacle to further development. A structure-based approach to circumvent the adduct formation culminated in the discovery of compound 11b ( TAK-931 ) possessing a quinuclidine moiety as a preclinical candidate. In this paper, the design, synthesis, and biological evaluation of this series of compounds will be presented.


  • Organizational Affiliation
    • Pharmaceutical Research Division , Takeda Pharmaceutical Company, Ltd. , 26-1, Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan.

Macromolecule Content 

  • Total Structure Weight: 185.5 kDa 
  • Atom Count: 12,788 
  • Modeled Residue Count: 1,574 
  • Deposited Residue Count: 1,620 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rho-associated protein kinase 2
A, B, C, D
405Homo sapiensMutation(s): 1 
Gene Names: ROCK2KIAA0619
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.39 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75116 (Homo sapiens)
Explore O75116 
Go to UniProtKB:  O75116
PHAROS:  O75116
GTEx:  ENSG00000134318 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75116
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O1S

Query on O1S



Download:Ideal Coordinates CCD File
E [auth A],
F [auth B]
6-(5-methyl-1H-pyrazol-4-yl)-2-[(pyrrolidin-1-yl)methyl]thieno[3,2-d]pyrimidin-4(3H)-one
C15 H17 N5 O S
MUYIKPWUBQUQAV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.225 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.456α = 90
b = 146.416β = 97.12
c = 111.876γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description