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9vve

Inhibition of PDE4 by Inhaled Small Molecules in COPD

Method: X-RAY DIFFRACTION D_max: 94.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vve
deposition_date	2025-07-15
last_revision	2026-05-27
title	Inhibition of PDE4 by Inhaled Small Molecules in COPD
keywords	PDE4 Inhibition, Small Molecules, COPD Therapy, Inhalation, PROTEIN BINDING; PROTEIN BINDING
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	29.51 Å
rg_electron	28.56 Å
i0	99748500.00
molecular_weight	77784.0 kDa
excluded_volume	96763 Å³
envelope_volume	118220 Å³
shell_volume	34193 Å³
envelope_diameter	96.4 Å
shell_rg	36.09 Å
envelope_rg	28.44 Å
shape_rg	28.51 Å
total_rg	29.42 Å
total_atoms	10724
n_residues	668
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	94.3 Å
rg_real	29.48 Å
rg_real_error	0.59 Å
i0_real	9.9750e+07
i0_real_error	1.4770e+06
rg_reciprocal	29.50 Å
i0_reciprocal	99750000.0000
total_estimate	0.9021
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	33.2 Å
skewness	0.288
kurtosis	-0.532
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	23560000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.949

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	;3',5'-cyclic-AMP phosphodiesterase 4B ;
formula_weight	43352.7 kDa
ec_number	3.1.4.53
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	10724

SISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIPQSPSPPLDEQNRDCQGLMEKFQFELTLDEEDSEGPEKEGEGHS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-[3,5-bis(chloranyl)pyridin-4-yl]-1-(2-chloranyl-8-methoxy-quinolin-5-yl)ethanone
formula_weight	381.6 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	66.679 Å
length_b	138.953 Å
length_c	216.685 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	3.510 Å
resolution_low	42.720 Å
r_factor	0.1760
r_work	0.1733
r_free	0.2280

fit	/app/data/saxs_computation/vv/9vve/9vve.fit
pddf	/app/data/pr_computation/vv/9vve/9vve.pr.out
profile	/app/data/saxs_computation/vv/9vve/9vve.dat

Inhibition of PDE4 by Inhaled Small Molecules in COPD

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction