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9vdd

The crystal structure of PDE4D with inhibitor LH17

Method: X-RAY DIFFRACTION D_max: 91.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vdd
deposition_date	2025-06-08
last_revision	2026-05-06
title	The crystal structure of PDE4D with inhibitor LH17
keywords	PDE4 inhibitor, 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	28.51 Å
rg_electron	27.82 Å
i0	175011000.00
molecular_weight	70041.0 kDa
excluded_volume	67649 Å³
envelope_volume	113980 Å³
shell_volume	33545 Å³
envelope_diameter	95.7 Å
shell_rg	35.65 Å
envelope_rg	27.76 Å
shape_rg	27.83 Å
total_rg	28.36 Å
total_atoms	5291
n_residues	645
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	91.1 Å
rg_real	28.45 Å
rg_real_error	0.58 Å
i0_real	1.7500e+08
i0_real_error	2.1750e+06
rg_reciprocal	28.48 Å
i0_reciprocal	175000000.0000
total_estimate	0.9029
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	30.9 Å
skewness	0.259
kurtosis	-0.554
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	26130000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.961

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;3',5'-cyclic-AMP phosphodiesterase 4D ;
formula_weight	37706.7 kDa
ec_number	3.1.4.53
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5370

TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 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	7-methoxy-8-(4-methoxyphenyl)-2,2-dimethyl-5-(pyridin-4-ylmethoxy)pyrano[3,2-g]chromen-6-one
formula_weight	471.5 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	79

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6. Citations (1)

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length_a	60.337 Å
length_b	78.334 Å
length_c	163.160 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	2.300 Å
resolution_low	23.170 Å
r_factor	0.2385
r_work	0.2354
r_free	0.2952

fit	/app/data/saxs_computation/vd/9vdd/9vdd.fit
pddf	/app/data/pr_computation/vd/9vdd/9vdd.pr.out
profile	/app/data/saxs_computation/vd/9vdd/9vdd.dat