5AXQ

Crystal structure of the catalytic domain of PDE10A complexed with highly potent and brain-penetrant PDE10A Inhibitor with 2-oxindole scaffold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design and synthesis of a novel 2-oxindole scaffold as a highly potent and brain-penetrant phosphodiesterase 10A inhibitor

Yoshikawa, M.Kamisaki, H.Kunitomo, J.Oki, H.Kokubo, H.Suzuki, A.Ikemoto, T.Nakashima, K.Kamiguchi, N.Harada, A.Kimura, H.Taniguchi, T.

(2015) Bioorg Med Chem 23: 7138-7149

  • DOI: 10.1016/j.bmc.2015.10.002
  • Primary Citation of Related Structures:  
    5AXQ, 5AXP

  • PubMed Abstract: 
  • Highly potent and brain-penetrant phosphodiesterase 10A (PDE10A) inhibitors based on the 2-oxindole scaffold were designed and synthesized. (2-Oxo-1,3-oxazolidin-3-yl)phenyl derivative 1 showed the high P-glycoprotein (P-gp) efflux (efflux ratio (ER) ...

    Highly potent and brain-penetrant phosphodiesterase 10A (PDE10A) inhibitors based on the 2-oxindole scaffold were designed and synthesized. (2-Oxo-1,3-oxazolidin-3-yl)phenyl derivative 1 showed the high P-glycoprotein (P-gp) efflux (efflux ratio (ER)=6.2) despite the potent PDE10A inhibitory activity (IC50=0.94 nM). We performed an optimization study to improve both the P-gp efflux ratio and PDE10A inhibitory activity by utilizing structure-based drug design (SBDD) techniques based on the X-ray crystal structure with PDE10A. Finally, 1-(cyclopropylmethyl)-4-fluoro-5-[5-methoxy-4-oxo-3-(1-phenyl-1H-pyrazol-5-yl)pyridazin-1(4H)-yl]-3,3-dimethyl-1,3-dihydro-2H-indol-2-one (19e) was identified with improved P-gp efflux (ER=1.4) and an excellent PDE10A inhibitory activity (IC50=0.080 nM). Compound 19e also exhibited satisfactory brain penetration, and suppressed PCP-induced hyperlocomotion with a minimum effective dose of 0.3mg/kg by oral administration in mice.


    Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10AAB338Homo sapiensMutation(s): 0 
Gene Names: PDE10A
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (PDB Primary Data)
Find proteins for Q9Y233 (Homo sapiens)
Explore Q9Y233 
Go to UniProtKB:  Q9Y233
NIH Common Fund Data Resources
PHAROS  Q9Y233
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4LP
Query on 4LP

Download CCD File 
A
1-(cyclopropylmethyl)-4-fluoranyl-5-[5-methoxy-4-oxidanylidene-3-(2-phenylpyrazol-3-yl)pyridazin-1-yl]-3,3-dimethyl-indol-2-one
C28 H26 F N5 O3
GKNWEXDLAOKVLQ-UHFFFAOYSA-N
 Ligand Interaction
4LK
Query on 4LK

Download CCD File 
B
3-[3-fluoranyl-4-[5-methoxy-4-oxidanylidene-3-(2-phenylpyrazol-3-yl)pyridazin-1-yl]phenyl]-1,3-oxazolidin-2-one
C23 H18 F N5 O4
OGYUWIMZDXHPEF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4LPIC50:  80   nM  Binding MOAD
4LKIC50:  0.9399999976158142   nM  BindingDB
4LPIC50:  0.07999999821186066   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.685α = 90
b = 81.793β = 90
c = 159.849γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-07-31 
  • Released Date: 2015-11-11 
  • Deposition Author(s): Oki, H., Zama, Y.

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Other