← Back to search

9zmg

Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 15

Method: X-RAY DIFFRACTION D_max: 68.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9zmg
deposition_date	2025-12-10
last_revision	2026-05-27
title	Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 15
keywords	HYDROLASE-INHIBITOR complex, PTP1B; HYDROLASE/INHIBITOR
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	20.18 Å
rg_electron	19.32 Å
i0	42293600.00
molecular_weight	33366.0 kDa
excluded_volume	32063 Å³
envelope_volume	51053 Å³
shell_volume	21676 Å³
envelope_diameter	71.0 Å
shell_rg	26.19 Å
envelope_rg	19.80 Å
shape_rg	19.31 Å
total_rg	20.02 Å
total_atoms	2510
n_residues	303
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	68.1 Å
rg_real	20.11 Å
rg_real_error	0.38 Å
i0_real	4.2290e+07
i0_real_error	5.8370e+05
rg_reciprocal	20.13 Å
i0_reciprocal	42290000.0000
total_estimate	0.6580
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	25.3 Å
skewness	0.288
kurtosis	-0.251
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	9209000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 0.406; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Tyrosine-protein phosphatase non-receptor type 1
formula_weight	38883.2 kDa
ec_number	3.1.3.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2753

MDYKDDDDKLEFMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	[(3-bromo-5-{[(pyridazin-3-yl)methyl]carbamoyl}-1-benzothiophen-2-yl)di(fluoro)methyl]phosphonic acid
formula_weight	478.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	243

▶

6. Citations (1)

▶

length_a	89.152 Å
length_b	89.152 Å
length_c	105.785 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	2.150 Å
resolution_low	25.020 Å
r_factor	0.2075
r_work	0.2052
r_free	0.2537

fit	/app/data/saxs_computation/zm/9zmg/9zmg.fit
pddf	/app/data/pr_computation/zm/9zmg/9zmg.pr.out
profile	/app/data/saxs_computation/zm/9zmg/9zmg.dat

Structure of PTP1b complexed with difluoromethylphosphonate inhibitor Compound 15

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