8XV3 | pdb_00008xv3

Crystal structure of the catalytic domain of human PDE10A complexed with (2-((4-(5-(2-methylpyridin-4-yl)-3-(trifluoromethyl)-1H-pyrazol-1-yl)phenoxy)methyl)quinolin-4-yl)(2,6-diazaspiro[3.3]heptan-2-yl)methanone

PDB DOI: https://doi.org/10.2210/pdb8XV3/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-14 Released: 2025-01-15
Deposition Author(s): Zhang, F.C., Huang, Y.Y., Luo, H.B., Guo, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.282 (Depositor), 0.285 (DCC)
R-Value Work:
0.236 (Depositor), 0.238 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure-based design and optimization of 3-trifluoromethyl-substituted pyrazoles as selective phosphodiesterase 10A inhibitors with improved metabolic stability to attenuate isoprenaline-induced cardiac hypertrophy

Zhang, F.C., Huang, Y.Y., Luo, H.B., Guo, L.

To be published.

Macromolecule Content

Total Structure Weight: 75.93 kDa
Atom Count: 5,336
Modeled Residue Count: 632
Deposited Residue Count: 644
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	322	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LWO (Subject of Investigation/LOI) Query on A1LWO Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	2,6-diazaspiro[3.3]heptan-2-yl-[2-[[4-[5-(2-methylpyridin-4-yl)-3-(trifluoromethyl)pyrazol-1-yl]phenoxy]methyl]quinolin-4-yl]methanone C₃₂ H₂₇ F₃ N₆ O₂ IFBZQSRPXWNBLJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.282 (Depositor), 0.285 (DCC)
R-Value Work: 0.236 (Depositor), 0.238 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.321	α = 90
b = 81.764	β = 90
c = 158.428	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22277154
National Natural Science Foundation of China (NSFC)	China	82003576
National Natural Science Foundation of China (NSFC)	China	82273856
National Natural Science Foundation of China (NSFC)	China	22277019