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9y8b

Human p38 ALPHA MAPK:MW164 pyridazine inhibitor complex

Method: X-RAY DIFFRACTION D_max: 74.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y8b
deposition_date	2025-09-11
last_revision	2025-09-24
title	Human p38 ALPHA MAPK:MW164 pyridazine inhibitor complex
keywords	;SERINE/THREONINE-PROTEIN KINASE, PROTEIN KINASE DOMAIN, TRANSFERASE, ATP BINDING, PHOSPHORYLATION, CYTOSOL, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX ;; TRANSFERASE/TRANSFERASE INHIBITOR
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	22.89 Å
rg_electron	21.87 Å
i0	24943100.00
molecular_weight	39466.0 kDa
excluded_volume	49902 Å³
envelope_volume	59019 Å³
shell_volume	22750 Å³
envelope_diameter	73.8 Å
shell_rg	28.45 Å
envelope_rg	22.03 Å
shape_rg	21.87 Å
total_rg	22.75 Å
total_atoms	5535
n_residues	338
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	74.2 Å
rg_real	22.86 Å
rg_real_error	0.34 Å
i0_real	2.4940e+07
i0_real_error	3.2240e+05
rg_reciprocal	22.87 Å
i0_reciprocal	24940000.0000
total_estimate	0.8964
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.1 Å
skewness	0.318
kurtosis	-0.356
angular_range	— – 0.3450 Å⁻¹
current_alpha	0.0001
highest_alpha	6927000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Mitogen-activated protein kinase 14
formula_weight	41343.2 kDa
ec_number	2.7.11.24
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5733

MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES

Source

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

Entity 2 non-polymer

description	4-[3-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]PYRIDINE
formula_weight	239.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	(3P)-6-(1-methylpiperidin-4-yl)-3-(naphthalen-2-yl)-4-(pyridin-4-yl)pyridazine
formula_weight	380.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	172

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6. Citations (1)

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length_a	67.039 Å
length_b	74.757 Å
length_c	79.510 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.970 Å
resolution_low	49.910 Å
r_factor	0.1831
r_work	0.1813
r_free	0.2208

fit	/app/data/saxs_computation/y8/9y8b/9y8b.fit
pddf	/app/data/pr_computation/y8/9y8b/9y8b.pr.out
profile	/app/data/saxs_computation/y8/9y8b/9y8b.dat

Human p38 ALPHA MAPK:MW164 pyridazine inhibitor complex

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