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9vq3

;Crystal structure of human phosphodiesterase 10A in complex with (6-fluoro-2-(1-(4-methylquinazolin-2-yl)azetidin-3-yl)imidazo[1,2-a]pyridin-3-yl)(4,7-diazaspiro[2.5]octan-7-yl)methanone ;

Method: X-RAY DIFFRACTION D_max: 93.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vq3
deposition_date	2025-07-04
last_revision	2026-02-04
title	;Crystal structure of human phosphodiesterase 10A in complex with (6-fluoro-2-(1-(4-methylquinazolin-2-yl)azetidin-3-yl)imidazo[1,2-a]pyridin-3-yl)(4,7-diazaspiro[2.5]octan-7-yl)methanone ;
keywords	PDE10, phosphodiesterase 10A, inbibitor, small molecular compound, pulmonary fibrosis, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	28.35 Å
rg_electron	27.72 Å
i0	165244000.00
molecular_weight	68392.0 kDa
excluded_volume	66222 Å³
envelope_volume	111210 Å³
shell_volume	33617 Å³
envelope_diameter	97.2 Å
shell_rg	35.00 Å
envelope_rg	27.64 Å
shape_rg	27.71 Å
total_rg	28.26 Å
total_atoms	5152
n_residues	631
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	93.7 Å
rg_real	28.38 Å
rg_real_error	0.64 Å
i0_real	1.6520e+08
i0_real_error	2.1710e+06
rg_reciprocal	28.37 Å
i0_reciprocal	165200000.0000
total_estimate	0.8856
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.8 Å
skewness	0.376
kurtosis	-0.380
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	20640000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.938

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;Isoform PDE10A2 of cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A ;
formula_weight	37160.8 kDa
ec_number	3.1.4.17
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5248

SICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	4,7-diazaspiro[2.5]octan-7-yl-[6-fluoranyl-2-[1-(4-methylquinazolin-2-yl)azetidin-3-yl]imidazo[1,2-a]pyridin-3-yl]methanone
formula_weight	471.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	96

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6. Citations (1)

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length_a	50.150 Å
length_b	81.651 Å
length_c	160.757 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.400 Å
resolution_low	25.780 Å
r_factor	0.2635
r_work	0.2610
r_free	0.3110

fit	/app/data/saxs_computation/vq/9vq3/9vq3.fit
pddf	/app/data/pr_computation/vq/9vq3/9vq3.pr.out
profile	/app/data/saxs_computation/vq/9vq3/9vq3.dat