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1c5y

STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR

Method: X-RAY DIFFRACTION D_max: 59.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1c5y
deposition_date	1999-12-22
title	STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR
keywords	selective, S1 site inhibitor, structure-based drug design, urokinase, trypsin, thrombin, BLOOD CLOTTING; BLOOD CLOTTING
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	18.47 Å
rg_electron	17.31 Å
i0	16135300.00
molecular_weight	29510.0 kDa
excluded_volume	36571 Å³
envelope_volume	40982 Å³
shell_volume	19198 Å³
envelope_diameter	60.2 Å
shell_rg	24.24 Å
envelope_rg	17.75 Å
shape_rg	17.30 Å
total_rg	18.33 Å
total_atoms	4073
n_residues	257
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	59.5 Å
rg_real	18.36 Å
rg_real_error	0.31 Å
i0_real	1.6140e+07
i0_real_error	1.8610e+05
rg_reciprocal	18.37 Å
i0_reciprocal	16140000.0000
total_estimate	0.8035
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	23.6 Å
skewness	0.169
kurtosis	-0.331
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	5274000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.817; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	PROTEIN (UROKINASE-TYPE PLASMINOGEN ACTIVATOR)
formula_weight	2708.2 kDa
ec_number	3.4.21.73
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5282

KPSSPPEELKFQCGQKTLRPRFK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Pichia pastoris

Entity 2 polymer

description	PROTEIN (UROKINASE-TYPE PLASMINOGEN ACTIVATOR)
formula_weight	28435.4 kDa
ec_number	3.4.21.73
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLMSPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTICLPSMYNDPQFGTSCEITGFGKEASTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKEENGLAL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Pichia pastoris

Entity 3 non-polymer

description	CITRATE ANION
formula_weight	189.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	THIENO[2,3-B]PYRIDINE-2-CARBOXAMIDINE
formula_weight	178.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	349

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6. Citations (1)

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length_a	82.070 Å
length_b	49.570 Å
length_c	66.320 Å
angle_alpha	90.00 °
angle_beta	113.20 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.650 Å
resolution_low	7.500 Å
r_factor	0.2000
r_work	0.2000
r_free	0.2460

fit	/app/data/saxs_computation/c5/1c5y/1c5y.fit
pddf	/app/data/pr_computation/c5/1c5y/1c5y.pr.out
profile	/app/data/saxs_computation/c5/1c5y/1c5y.dat

STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)