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9s1n

Crystal structure of DNPH1 bound by compound 19

Method: X-RAY DIFFRACTION D_max: 46.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s1n
deposition_date	2025-07-18
title	Crystal structure of DNPH1 bound by compound 19
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	15.18 Å
rg_electron	14.00 Å
i0	8738860.00
molecular_weight	14471.0 kDa
excluded_volume	13903 Å³
envelope_volume	21361 Å³
shell_volume	12871 Å³
envelope_diameter	45.4 Å
shell_rg	19.87 Å
envelope_rg	14.20 Å
shape_rg	13.97 Å
total_rg	14.91 Å
total_atoms	1095
n_residues	140
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	46.6 Å
rg_real	15.05 Å
rg_real_error	0.22 Å
i0_real	8.7390e+06
i0_real_error	9.3460e+04
rg_reciprocal	15.06 Å
i0_reciprocal	8739000.0000
total_estimate	0.8963
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	20.1 Å
skewness	0.079
kurtosis	-0.452
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	1865000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.977

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	5-hydroxymethyl-dUMP N-hydrolase
formula_weight	17174.3 kDa
ec_number	3.2.2.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1203

MRPALYFCGSIRGGREDRTLYERIVSRLRRFGTVLTEHVAAAELGARGEEAAGGDRLIHEQDLEWLQQADVVVAEVTQPSLGVGYELGRAVAFNKRILCLFRPQSGRVLSAMIRGAADGSRFQVWDYEEGEVEALLDRYFEADPLEENLYFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	;2-[[3-(7-bromanyl-1,2,4,5-tetrahydro-3-benzazepin-3-yl)-1,2,4-oxadiazol-5-yl]methyl]-3,4-dihydro-1~{H}-isoquinoline-7-carboxylic acid ;
formula_weight	483.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	90

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6. Citations (1)

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length_a	47.026 Å
length_b	84.522 Å
length_c	33.839 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	1.503 Å
resolution_low	42.260 Å
r_factor	0.2105
r_work	0.2096
r_free	0.2289

fit	/app/data/saxs_computation/s1/9s1n/9s1n.fit
pddf	/app/data/pr_computation/s1/9s1n/9s1n.pr.out
profile	/app/data/saxs_computation/s1/9s1n/9s1n.dat

Crystal structure of DNPH1 bound by compound 19

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