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9s0o

Crystal structure of DNPH1 bound by compound 6

Method: X-RAY DIFFRACTION D_max: 63.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s0o
deposition_date	2025-07-16
title	Crystal structure of DNPH1 bound by compound 6
keywords	DNA damage response, inhibitor, drug discovery, 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	19.22 Å
rg_electron	18.32 Å
i0	27422500.00
molecular_weight	27083.0 kDa
excluded_volume	26256 Å³
envelope_volume	40594 Å³
shell_volume	18645 Å³
envelope_diameter	64.9 Å
shell_rg	24.41 Å
envelope_rg	18.56 Å
shape_rg	18.31 Å
total_rg	18.96 Å
total_atoms	2059
n_residues	258
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	63.8 Å
rg_real	19.17 Å
rg_real_error	0.36 Å
i0_real	2.7420e+07
i0_real_error	3.5350e+05
rg_reciprocal	19.18 Å
i0_reciprocal	27420000.0000
total_estimate	0.8777
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.1 Å
skewness	0.341
kurtosis	-0.239
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	6621000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.987

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	5-hydroxymethyl-dUMP N-hydrolase
formula_weight	17174.3 kDa
ec_number	3.2.2.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2244

MRPALYFCGSIRGGREDRTLYERIVSRLRRFGTVLTEHVAAAELGARGEEAAGGDRLIHEQDLEWLQQADVVVAEVTQPSLGVGYELGRAVAFNKRILCLFRPQSGRVLSAMIRGAADGSRFQVWDYEEGEVEALLDRYFEADPLEENLYFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-[[2-[methyl-[2-(4-phenylphenyl)ethyl]amino]-1,3-thiazol-4-yl]methyl]-3,4-dihydro-1~{H}-isoquinoline-7-carboxylic acid
formula_weight	483.6 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	164

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6. Citations (1)

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length_a	89.436 Å
length_b	54.750 Å
length_c	57.388 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	1.514 Å
resolution_low	18.710 Å
r_factor	0.2074
r_work	0.2055
r_free	0.2441

fit	/app/data/saxs_computation/s0/9s0o/9s0o.fit
pddf	/app/data/pr_computation/s0/9s0o/9s0o.pr.out
profile	/app/data/saxs_computation/s0/9s0o/9s0o.dat

Crystal structure of DNPH1 bound by compound 6

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