5DH5 | pdb_00005dh5

PDE10 complexed with N-[(1-methylpyrazol-4-yl)methyl]-5-[[(1S,2S)-2-(2-pyridyl)cyclopropyl]methoxy]pyrazolo[1,5-a]pyrimidin-7-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.233 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5DH5

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of pyrazolopyrimidine phosphodiesterase 10A inhibitors for the treatment of schizophrenia.

Raheem, I.T.Schreier, J.D.Fuerst, J.Gantert, L.Hostetler, E.D.Huszar, S.Joshi, A.Kandebo, M.Kim, S.H.Li, J.Ma, B.McGaughey, G.Sharma, S.Shipe, W.D.Uslaner, J.Vandeveer, G.H.Yan, Y.Renger, J.J.Smith, S.M.Coleman, P.J.Cox, C.D.

(2016) Bioorg Med Chem Lett 26: 126-132

  • DOI: https://doi.org/10.1016/j.bmcl.2015.11.013
  • Primary Citation Related Structures: 
    5DH4, 5DH5

  • PubMed Abstract: 

    Herein, we present the identification of a novel class of pyrazolopyrimidine phosphodiesterase 10A (PDE10A) inhibitors. Beginning with a lead molecule (1) identified through a fragment-based drug discovery (FBDD) effort, lead optimization was enabled by rational design, X-ray crystallography, metabolic and off-target profiling, and fragment scaffold-hopping. We highlight the discovery of PyP-1, a potent, highly selective, and orally bioavailable pyrazolopyrimidine inhibitor of PDE10A. PyP-1 exhibits sub-nanomolar potency (PDE10A Ki=0.23nM), excellent pharmacokinetic (PK) and physicochemical properties, and a clean off-target profile. It displays dose-dependent efficacy in numerous pharmacodynamic (PD) assays that measure potential for anti-psychotic activity and cognitive improvement. PyP-1 also has a clean preclinical profile with respect to cataleptic potential in rats, prolactin secretion, and weight gain, common adverse events associated with currently marketed therapeutics. Further, PyP-1 displays in vivo preclinical target engagement as measured by PET enzyme occupancy in concert with [(11)C]MK-8193, a novel PDE10A PET tracer.


  • Organizational Affiliation
    • Discovery Chemistry, Merck Research Laboratories, West Point, PA 19486, United States.

Macromolecule Content 

  • Total Structure Weight: 80.14 kDa 
  • Atom Count: 5,406 
  • Modeled Residue Count: 644 
  • Deposited Residue Count: 690 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
A, B
345Homo sapiensMutation(s): 0 
Gene Names: PDE10A
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y233 (Homo sapiens)
Explore Q9Y233 
Go to UniProtKB:  Q9Y233
PHAROS:  Q9Y233
GTEx:  ENSG00000112541 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y233
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5AY

Query on 5AY



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
N-[(1-methyl-1H-pyrazol-4-yl)methyl]-5-{[(1S,2S)-2-(pyridin-2-yl)cyclopropyl]methoxy}pyrazolo[1,5-a]pyrimidin-7-amine
C20 H21 N7 O
YLPZTDCVMOWRPZ-CVEARBPZSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5AY BindingDB:  5DH5 Ki: min: 0.23, max: 0.32 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.233 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.51α = 90
b = 81.78β = 90
c = 158.96γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-01-27 
  • Deposition Author(s): Yan, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations