4TPM | pdb_00004tpm

Crystal structure of 2-(3-alkoxy-1-azetidinyl) quinolines as PDE10A Inhibitors

PDB DOI: https://doi.org/10.2210/pdb4TPM/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-08 Released: 2014-12-17
Deposition Author(s): Chmait, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free:
0.179 (Depositor), 0.188 (DCC)
R-Value Work:
0.151 (Depositor), 0.164 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Synthesis and preliminary biological evaluation of potent and selective 2-(3-alkoxy-1-azetidinyl) quinolines as novel PDE10A inhibitors with improved solubility.

Rzasa, R.M., Frohn, M.J., Andrews, K.L., Chmait, S., Chen, N., Clarine, J.G., Davis, C., Eastwood, H.A., Horne, D.B., Hu, E., Jones, A.D., Kaller, M.R., Kunz, R.K., Miller, S., Monenschein, H., Nguyen, T., Pickrell, A.J., Porter, A., Reichelt, A., Zhao, X., Treanor, J.J., Allen, J.R.

(2014) Bioorg Med Chem 22: 6570-6585

PubMed: 25456383 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2014.10.013
Primary Citation Related Structures:
4TPM, 4TPP

PubMed Abstract:
We report the discovery of a novel series of 2-(3-alkoxy-1-azetidinyl) quinolines as potent and selective PDE10A inhibitors. Structure-activity studies improved the solubility (pH 7.4) and maintained high PDE10A activity compared to initial lead compound 3, with select compounds demonstrating good oral bioavailability. X-ray crystallographic studies revealed two distinct binding modes to the catalytic site of the PDE10A enzyme. An ex vivo receptor occupancy assay in rats demonstrated that this series of compounds covered the target within the striatum.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 83.63 kDa
Atom Count: 5,146
Modeled Residue Count: 610
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	A, B	351	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y233
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
35E Query on 35E Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain U [auth B] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B] mmCIF format, chain K [auth A] mmCIF format, chain U [auth B]	K [auth A], U [auth B]	[1-(3-{[1-(quinolin-2-yl)azetidin-3-yl]oxy}pyrazin-2-yl)piperidin-4-yl]methanol C₂₂ H₂₅ N₅ O₂ VIXNRMUNIQTMQR-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain U [auth B] Interactions & Density Focus chain K [auth A] Focus chain U [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain N [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] 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 N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] 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 N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain M [auth A]	L [auth A], M [auth A], V [auth B], W [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain V [auth B] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.179 (Depositor), 0.188 (DCC)
R-Value Work: 0.151 (Depositor), 0.164 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 253.878	α = 90
b = 253.878	β = 90
c = 253.878	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-12-17

Deposition Author(s):

Chmait, S.

Revision History (Full details and data files)

Version 1.0: 2014-12-17
Type: Initial release
Version 1.1: 2015-10-14
Changes: Data collection
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-11-13
Changes: Structure summary

4TPM | pdb_00004tpm

Crystal structure of 2-(3-alkoxy-1-azetidinyl) quinolines as PDE10A Inhibitors

Literature

Synthesis and preliminary biological evaluation of potent and selective 2-(3-alkoxy-1-azetidinyl) quinolines as novel PDE10A inhibitors with improved solubility.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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