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9tkt

Mapping the SHP2 allosteric pocket with target-biased covalent fragments

Method: X-RAY DIFFRACTION D_max: 129.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tkt
deposition_date	2025-12-10
last_revision	2026-05-06
title	Mapping the SHP2 allosteric pocket with target-biased covalent fragments
keywords	SHP2 allosteric site, Aryl sulfonyl fluoride warheads, SF12a, CYTOSOLIC PROTEIN; CYTOSOLIC PROTEIN
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	37.28 Å
rg_electron	37.15 Å
i0	396500000.00
molecular_weight	106240.0 kDa
excluded_volume	101930 Å³
envelope_volume	188680 Å³
shell_volume	43536 Å³
envelope_diameter	133.9 Å
shell_rg	41.37 Å
envelope_rg	37.42 Å
shape_rg	37.12 Å
total_rg	37.40 Å
total_atoms	8043
n_residues	989
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	129.6 Å
rg_real	37.55 Å
rg_real_error	1.47 Å
i0_real	3.9650e+08
i0_real_error	6.6010e+06
rg_reciprocal	37.39 Å
i0_reciprocal	396400000.0000
total_estimate	0.8548
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	40.1 Å
skewness	0.501
kurtosis	-0.259
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	33540000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.916; Smooth: 0.808

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Tyrosine-protein phosphatase non-receptor type 11
formula_weight	60116.8 kDa
ec_number	3.1.3.48
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8238

TSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL

Source

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

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	;3-[(1S)-1-azanylspiro[1,3-dihydroindene-2,4'-piperidine]-1'-yl]carbonylbenzenesulfonic acid ;
formula_weight	386.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	119

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6. Citations (1)

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length_a	44.930 Å
length_b	212.540 Å
length_c	55.490 Å
angle_alpha	90.00 °
angle_beta	95.23 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.350 Å
resolution_low	49.027 Å
r_factor	—
r_work	0.2405
r_free	0.2831

fit	/app/data/saxs_computation/tk/9tkt/9tkt.fit
pddf	/app/data/pr_computation/tk/9tkt/9tkt.pr.out
profile	/app/data/saxs_computation/tk/9tkt/9tkt.dat

Mapping the SHP2 allosteric pocket with target-biased covalent fragments

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