← Back to search

1c5l

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

Method: X-RAY DIFFRACTION D_max: 60.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1c5l
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-HYDROLASE INHIBITOR COMPLEX; BLOOD CLOTTING/HYDROLASE INHIBITOR
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	19.61 Å
rg_electron	18.33 Å
i0	20780900.00
molecular_weight	34496.0 kDa
excluded_volume	43087 Å³
envelope_volume	49641 Å³
shell_volume	21784 Å³
envelope_diameter	61.9 Å
shell_rg	25.48 Å
envelope_rg	18.61 Å
shape_rg	18.32 Å
total_rg	19.34 Å
total_atoms	4791
n_residues	297
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

▼

3. P(r) Analysis (GNOM)

dmax	60.8 Å
rg_real	19.43 Å
rg_real_error	0.30 Å
i0_real	2.0780e+07
i0_real_error	2.4890e+05
rg_reciprocal	19.46 Å
i0_reciprocal	20780000.0000
total_estimate	0.8923
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.7 Å
skewness	0.079
kurtosis	-0.459
angular_range	— – 0.4050 Å⁻¹
current_alpha	0.0000
highest_alpha	8059000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.982

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	thrombin
formula_weight	4096.5 kDa
ec_number	3.4.21.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L
atom_count	5751

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 polymer

description	thrombin
formula_weight	29780.2 kDa
ec_number	3.4.21.5
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Entity 3 polymer

description	Hirudin
formula_weight	1363.4 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

DFEEIPEEYL

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	293

▶

6. Citations (1)

▶

length_a	72.370 Å
length_b	73.520 Å
length_c	73.850 Å
angle_alpha	90.00 °
angle_beta	100.93 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.470 Å
resolution_low	7.500 Å
r_factor	0.2150
r_work	0.2150
r_free	0.2360

fit	/app/data/saxs_computation/c5/1c5l/1c5l.fit
pddf	/app/data/pr_computation/c5/1c5l/1c5l.pr.out
profile	/app/data/saxs_computation/c5/1c5l/1c5l.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 (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)