4HF4

Crystal Structure of PDE10A with a biaryl ether inhibitor (1-(1-(3-(4-(benzo[d]thiazol-2-ylamino)phenoxy)pyrazin-2-yl)piperidin-4-yl)ethanol)

PDB DOI: https://doi.org/10.2210/pdb4HF4/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.197
R-Value Work: 0.176
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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

PubMed: 23149228 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2012.10.078
Primary Citation of Related Structures:
4HEU, 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 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

Macromolecule Content

Total Structure Weight: 76.4 kDa
Atom Count: 5,745
Modelled Residue Count: 626
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	A, B	318	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y233
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
15H Query on 15H Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain X [auth B] MOL2 format, chain N [auth A] MOL2 format, chain X [auth B] mmCIF format, chain N [auth A] mmCIF format, chain X [auth B]	N [auth A], X [auth B]	(1S)-1-(1-{3-[4-(1,3-benzothiazol-2-ylamino)phenoxy]pyrazin-2-yl}piperidin-4-yl)ethanol C₂₄ H₂₅ N₅ O₂ S GNWKATFENPQMIQ-INIZCTEOSA-N		Interactions Focus chain N [auth A] Focus chain X [auth B] Interactions & Density Focus chain N [auth A] Focus chain X [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain G [auth A] MOL2 format, chain T [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain G [auth A] mmCIF format, chain T [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	C [auth A], D [auth A], O [auth B], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain O [auth B] Focus chain P [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
15H	PDBBind: 4HF4	Ki: 2.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.197
R-Value Work: 0.176
R-Value Observed: 0.177
Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 252.879	α = 90
b = 252.879	β = 90
c = 252.879	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-12-12

Deposition Author(s):

Chmait, S.

Jordan, S.

Revision History (Full details and data files)

Version 1.0: 2012-12-12
Type: Initial release
Version 1.1: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary