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9s1o

Crystal structure of DNPH1 bound by compound 18

Method: X-RAY DIFFRACTION D_max: 62.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s1o
deposition_date	2025-07-18
title	Crystal structure of DNPH1 bound by compound 18
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	19.09 Å
rg_electron	18.24 Å
i0	26919100.00
molecular_weight	26672.0 kDa
excluded_volume	25801 Å³
envelope_volume	40288 Å³
shell_volume	18586 Å³
envelope_diameter	62.6 Å
shell_rg	24.35 Å
envelope_rg	18.48 Å
shape_rg	18.23 Å
total_rg	18.91 Å
total_atoms	2024
n_residues	250
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	62.5 Å
rg_real	19.06 Å
rg_real_error	0.31 Å
i0_real	2.6920e+07
i0_real_error	3.2630e+05
rg_reciprocal	19.06 Å
i0_reciprocal	26920000.0000
total_estimate	0.8822
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.363
kurtosis	-0.210
angular_range	— – 0.4150 Å⁻¹
current_alpha	0.0000
highest_alpha	7638000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.991

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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	2120

MRPALYFCGSIRGGREDRTLYERIVSRLRRFGTVLTEHVAAAELGARGEEAAGGDRLIHEQDLEWLQQADVVVAEVTQPSLGVGYELGRAVAFNKRILCLFRPQSGRVLSAMIRGAADGSRFQVWDYEEGEVEALLDRYFEADPLEENLYFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	;2-[[2-[(1~{R},5~{S})-7-phenyl-3,7-diazabicyclo[3.3.1]nonan-3-yl]-1,3-thiazol-4-yl]methyl]-3,4-dihydro-1~{H}-isoquinoline-7-carboxylic acid ;
formula_weight	474.6 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	96

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6. Citations (1)

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length_a	149.345 Å
length_b	149.345 Å
length_c	53.965 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 6 2 2
int_tables_number	177
crystal_system	—

resolution	1.768 Å
resolution_low	19.340 Å
r_factor	0.2366
r_work	0.2354
r_free	0.2584

fit	/app/data/saxs_computation/s1/9s1o/9s1o.fit
pddf	/app/data/pr_computation/s1/9s1o/9s1o.pr.out
profile	/app/data/saxs_computation/s1/9s1o/9s1o.dat

Crystal structure of DNPH1 bound by compound 18

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