4PHW | pdb_00004phw

Crystal Structure of PDE10A with 1H-benzimidazol-2-yl(4-((3-(tetrahydro-2H-pyran-4-yl)-2-pyridinyl)oxy)phenyl)methanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.180 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2W1Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Discovery of Clinical Candidate 1-(4-(3-(4-(1H-Benzo[d]imidazole-2-carbonyl)phenoxy)pyrazin-2-yl)piperidin-1-yl)ethanone (AMG 579), A Potent, Selective, and Efficacious Inhibitor of Phosphodiesterase 10A (PDE10A).

Hu, E.Chen, N.Bourbeau, M.P.Harrington, P.E.Biswas, K.Kunz, R.K.Andrews, K.L.Chmait, S.Zhao, X.Davis, C.Ma, J.Shi, J.Lester-Zeiner, D.Danao, J.Able, J.Cueva, M.Talreja, S.Kornecook, T.Chen, H.Porter, A.Hungate, R.Treanor, J.Allen, J.R.

(2014) J Med Chem 57: 6632-6641

  • DOI: https://doi.org/10.1021/jm500713j
  • Primary Citation of Related Structures:  
    4PHW

  • PubMed Abstract: 

    We report the identification of a PDE10A clinical candidate by optimizing potency and in vivo efficacy of promising keto-benzimidazole leads 1 and 2. Significant increase in biochemical potency was observed when the saturated rings on morpholine 1 and N-acetyl piperazine 2 were changed by a single atom to tetrahydropyran 3 and N-acetyl piperidine 5. A second single atom modification from pyrazines 3 and 5 to pyridines 4 and 6 improved the inhibitory activity of 4 but not 6. In the in vivo LC-MS/MS target occupancy (TO) study at 10 mg/kg, 3, 5, and 6 achieved 86-91% occupancy of PDE10A in the brain. Furthermore, both CNS TO and efficacy in PCP-LMA behavioral model were observed in a dose dependent manner. With superior in vivo TO, in vivo efficacy and in vivo PK profiles in multiple preclinical species, compound 5 (AMG 579) was advanced as our PDE10A clinical candidate.


  • Organizational Affiliation

    Department of Medicinal Chemistry, ‡Department of Molecular Structure and Characterization, §Department of Pharmacokinetics and Drug Metabolism, ∥Department of Neuroscience, Amgen Inc. , One Amgen Center Drive, Thousand Oaks, California 93012-1799, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
A, B
351Homo 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
2W1
Query on 2W1

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B]
1H-benzimidazol-2-yl(4-{[3-(tetrahydro-2H-pyran-4-yl)pyridin-2-yl]oxy}phenyl)methanone
C24 H21 N3 O3
NQQHFVCQMJVYTB-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth B]
K [auth B]
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.180 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 253.34α = 90
b = 253.34β = 90
c = 253.34γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2W1Click on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2014-08-06 
  • Deposition Author(s): Chmait, S.

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2024-10-30
    Changes: Structure summary