← Back to search

11ad

Structural basis for high-affinity inhibitor binding to lipid kinases PIP4K2A and PIP4K2B

Method: X-RAY DIFFRACTION D_max: 71.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	11ad
deposition_date	2026-02-13
title	Structural basis for high-affinity inhibitor binding to lipid kinases PIP4K2A and PIP4K2B
keywords	Kinase, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	21.28 Å
rg_electron	20.30 Å
i0	41897300.00
molecular_weight	33672.0 kDa
excluded_volume	32708 Å³
envelope_volume	54861 Å³
shell_volume	22501 Å³
envelope_diameter	75.4 Å
shell_rg	26.92 Å
envelope_rg	20.58 Å
shape_rg	20.25 Å
total_rg	21.04 Å
total_atoms	2547
n_residues	317
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	71.0 Å
rg_real	21.20 Å
rg_real_error	0.44 Å
i0_real	4.1900e+07
i0_real_error	5.3120e+05
rg_reciprocal	21.22 Å
i0_reciprocal	41900000.0000
total_estimate	0.8029
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.1 Å
skewness	0.284
kurtosis	-0.291
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	8853000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
formula_weight	43114.7 kDa
ec_number	2.7.1.149
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2751

GSHMASDPLLSVLMWGVNHSINELSHVQIPVMLMPDDFKAYSKIKVDNHLFNKENMPSHFKFKEYCPMVFRNLRERFGIDDQDFQNSLTRSAPLPNDSQARSGARFHTSYDKRYIIKTITSEDVAEMHNILKKYHQYIVECHGITLLPQFLGMYRLNVDGVEIYVIVTRNVFSHRLSVYRKYDLKGSTVAREASDKEKAKELPTLKDNDFINEGQKIYIDDNNKKVFLEKLKKDVEFLAQLKLMDYSLLVGIHDVERAEQEEVECEENDGEEEGESDGTHPVGTPPDSPGNTLNSSPPLAPGEFDPNIDVYGIKCHENSPRKEVYFMAIIDILTHYDAKKKAAHAAKTVKHGAGAEISTVNPEQYSKRFLDFIGHIL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	(7R)-8-cyclopentyl-2-(3,5-dichloro-4-hydroxyanilino)-5-methyl-7-[(pyridin-2-yl)methyl]-7,8-dihydropteridin-6(5H)-one
formula_weight	499.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	204

▶

6. Citations (1)

▶

length_a	135.883 Å
length_b	135.883 Å
length_c	94.679 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	2.790 Å
resolution_low	32.440 Å
r_factor	0.1726
r_work	0.1694
r_free	0.2337

fit	/app/data/saxs_computation/1a/11ad/11ad.fit
pddf	/app/data/pr_computation/1a/11ad/11ad.pr.out
profile	/app/data/saxs_computation/1a/11ad/11ad.dat

Structural basis for high-affinity inhibitor binding to lipid kinases PIP4K2A and PIP4K2B

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