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9s04

PYCR1 in complex with 1-(2,4-Difluorophenyl)-2-(1H-1,2,4-triazol-1- yl)ethanone

Method: X-RAY DIFFRACTION D_max: 118.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s04
deposition_date	2025-07-16
last_revision	2025-10-15
title	PYCR1 in complex with 1-(2,4-Difluorophenyl)-2-(1H-1,2,4-triazol-1- yl)ethanone
keywords	;delta-1-pyrroline-5-carboxylate reductase, PYCR1, cancer, crystallographic fragment screening (XFS), molecular docking, inhibitors, proline metabolism, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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	36.72 Å
rg_electron	36.24 Å
i0	640704000.00
molecular_weight	134890.0 kDa
excluded_volume	129130 Å³
envelope_volume	233670 Å³
shell_volume	53449 Å³
envelope_diameter	121.6 Å
shell_rg	42.75 Å
envelope_rg	36.01 Å
shape_rg	36.24 Å
total_rg	36.55 Å
total_atoms	10179
n_residues	1365
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	118.5 Å
rg_real	36.61 Å
rg_real_error	0.95 Å
i0_real	6.4070e+08
i0_real_error	1.1140e+07
rg_reciprocal	36.68 Å
i0_reciprocal	640700000.0000
total_estimate	0.8945
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.6 Å
skewness	0.215
kurtosis	-0.450
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	143800000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.916

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Isoform 3 of Pyrroline-5-carboxylate reductase 1, mitochondrial
formula_weight	36075.5 kDa
ec_number	1.5.1.2
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	11114

MHHHHHHSSGVDLGTENNLYFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLESGGFRSLLINAVEASCIRTRELQSMADQEQVSPAAIKKTILDKVKLDSPAGTALSPSGHTKLLPRSLAPAGKD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	L(+)-TARTARIC ACID
formula_weight	150.1 kDa
src_method	syn
entity_count	5

Entity 3 non-polymer

description	1-[2,4-bis(fluoranyl)phenyl]-2-(1,2,4-triazol-1-yl)ethanone
formula_weight	223.2 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	6

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	842

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6. Citations (1)

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length_a	163.780 Å
length_b	88.001 Å
length_c	116.812 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	20

space_group	P 21 21 2
int_tables_number	18
crystal_system	orthorhombic

resolution	1.570 Å
resolution_low	38.640 Å
r_factor	0.1850
r_work	0.1848
r_free	0.2052

fit	/app/data/saxs_computation/s0/9s04/9s04.fit
pddf	/app/data/pr_computation/s0/9s04/9s04.pr.out
profile	/app/data/saxs_computation/s0/9s04/9s04.dat