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9s21

Crystal structure of human SIRT2 in complex with SirReal-triazole inhibitor LG023

Method: X-RAY DIFFRACTION D_max: 72.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s21
deposition_date	2025-07-21
title	Crystal structure of human SIRT2 in complex with SirReal-triazole inhibitor LG023
keywords	Sirtuins, Inhibitor, Deacetylation, 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	21.00 Å
rg_electron	20.24 Å
i0	36004800.00
molecular_weight	31205.0 kDa
excluded_volume	30284 Å³
envelope_volume	49847 Å³
shell_volume	20836 Å³
envelope_diameter	70.3 Å
shell_rg	26.48 Å
envelope_rg	20.50 Å
shape_rg	20.22 Å
total_rg	20.91 Å
total_atoms	2353
n_residues	291
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	72.0 Å
rg_real	20.98 Å
rg_real_error	0.43 Å
i0_real	3.6000e+07
i0_real_error	4.9720e+05
rg_reciprocal	20.99 Å
i0_reciprocal	36000000.0000
total_estimate	0.8710
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.0 Å
skewness	0.351
kurtosis	-0.344
angular_range	— – 0.3800 Å⁻¹
current_alpha	0.0000
highest_alpha	6634000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 1.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	NAD-dependent protein deacetylase sirtuin-2
formula_weight	34416.7 kDa
ec_number	3.5.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2585

GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-~{N}-[5-[[3-(1~{H}-1,2,3-triazol-4-ylmethoxy)phenyl]methyl]-1,3-thiazol-2-yl]ethanamide
formula_weight	467.6 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	(R,R)-2,3-BUTANEDIOL
formula_weight	90.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	218

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6. Citations (1)

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length_a	35.949 Å
length_b	73.910 Å
length_c	55.495 Å
angle_alpha	90.00 °
angle_beta	95.06 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.550 Å
resolution_low	44.270 Å
r_factor	0.1735
r_work	0.1719
r_free	0.2036

fit	/app/data/saxs_computation/s2/9s21/9s21.fit
pddf	/app/data/pr_computation/s2/9s21/9s21.pr.out
profile	/app/data/saxs_computation/s2/9s21/9s21.dat