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9szn

Crystal structure of the catalytic domain of USP7 in complex with Compound 43

Method: X-RAY DIFFRACTION D_max: 87.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9szn
deposition_date	2025-10-15
title	Crystal structure of the catalytic domain of USP7 in complex with Compound 43
keywords	USP7 INHIBITOR COMPLEX, STRUCTURE-GUIDED DRUG DESIGN, CANCER, 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	22.47 Å
rg_electron	21.56 Å
i0	49099400.00
molecular_weight	36206.0 kDa
excluded_volume	34894 Å³
envelope_volume	59138 Å³
shell_volume	23141 Å³
envelope_diameter	90.4 Å
shell_rg	28.21 Å
envelope_rg	22.46 Å
shape_rg	21.53 Å
total_rg	22.25 Å
total_atoms	2735
n_residues	326
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	87.4 Å
rg_real	22.51 Å
rg_real_error	0.79 Å
i0_real	4.9100e+07
i0_real_error	7.5630e+05
rg_reciprocal	22.50 Å
i0_reciprocal	49100000.0000
total_estimate	0.7951
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.5 Å
skewness	0.514
kurtosis	0.235
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	7065000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.490; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.865; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Ubiquitin carboxyl-terminal hydrolase 7
formula_weight	41068.3 kDa
ec_number	3.4.19.12
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3072

KKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQKRKERQE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;3-((7-(3-((S)-3-aminopyrrolidine-1-carbonyl)-4-methyl-6-(trifluoromethyl)pyridin-2-yl)thieno[3,2-b]pyridin-2-yl)methyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2,4-dione ;
formula_weight	557.6 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	289

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6. Citations (1)

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length_a	51.890 Å
length_b	141.000 Å
length_c	124.190 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.990 Å
resolution_low	30.650 Å
r_factor	0.1859
r_work	0.1837
r_free	0.2263

fit	/app/data/saxs_computation/sz/9szn/9szn.fit
pddf	/app/data/pr_computation/sz/9szn/9szn.pr.out
profile	/app/data/saxs_computation/sz/9szn/9szn.dat

Crystal structure of the catalytic domain of USP7 in complex with Compound 43

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