4HEU

Crystal Structure of PDE10A with a biaryl ether inhibitor ((1-(3-(4-((1H-benzo[d]imidazol-2-yl)amino)phenoxy)pyridin-2-yl)piperidin-4-yl)methanol)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of selective biaryl ethers as PDE10A inhibitors: Improvement in potency and mitigation of Pgp-mediated efflux.

Rzasa, R.M.Hu, E.Rumfelt, S.Chen, N.Andrews, K.L.Chmait, S.Falsey, J.R.Zhong, W.Jones, A.D.Porter, A.Louie, S.W.Zhao, X.Treanor, J.J.Allen, J.R.

(2012) Bioorg.Med.Chem.Lett. 22: 7371-7375

  • DOI: 10.1016/j.bmcl.2012.10.078
  • Primary Citation of Related Structures:  4HF4

  • PubMed Abstract: 
  • We report the discovery of a novel series of biaryl ethers as potent and selective PDE10A inhibitors. Structure-activity studies improved the potency and decreased Pgp-mediated efflux found in the initial compound 4. X-ray crystallographic studies re ...

    We report the discovery of a novel series of biaryl ethers as potent and selective PDE10A inhibitors. Structure-activity studies improved the potency and decreased Pgp-mediated efflux found in the initial compound 4. X-ray crystallographic studies revealed two novel binding modes to the catalytic site of the PDE10A enzyme.


    Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA. rrzasa@amgen.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
A, B
318Homo sapiensGene Names: PDE10A
EC: 3.1.4.35, 3.1.4.17
Find proteins for Q9Y233 (Homo sapiens)
Go to Gene View: PDE10A
Go to UniProtKB:  Q9Y233
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
15J
Query on 15J

Download SDF File 
Download CCD File 
A, B
(1-{3-[4-(1H-benzimidazol-2-ylamino)phenoxy]pyridin-2-yl}piperidin-4-yl)methanol
C24 H25 N5 O2
XGFBQNCOZRNUGL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
15JIC50: 0.1 nM (100) BINDINGDB
15JIC50: 422 nM BINDINGMOAD
15JIC50: 0.097 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.186 
  • Space Group: F 2 3
Unit Cell:
Length (Å)Angle (°)
a = 252.859α = 90.00
b = 252.859β = 90.00
c = 252.859γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
ADSCdata collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-10-04 
  • Released Date: 2012-12-12 
  • Deposition Author(s): Chmait, S., Jordan, S.

Revision History 

  • Version 1.0: 2012-12-12
    Type: Initial release