SAXSdb — 9z4x

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1. Structure Basics

entry_id	9z4x
deposition_date	2025-11-11
last_revision	2025-11-26
title	MENIN IN COMPLEX WITH JNJ-75276617 (Bleximenib)
keywords	MENIN, MEN1, MLL, TRANSCRIPTION, INHIBITOR COMPLEX, Bleximenib, TRANSCRIPTION-INHIBITOR complex; TRANSCRIPTION/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	49.28 Å
rg_electron	49.51 Å
i0	1343060000.00
molecular_weight	203590.0 kDa
excluded_volume	197910 Å³
envelope_volume	405520 Å³
shell_volume	70155 Å³
envelope_diameter	189.5 Å
shell_rg	50.40 Å
envelope_rg	49.17 Å
shape_rg	49.50 Å
total_rg	49.54 Å
total_atoms	15463
n_residues	1936
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	178.2 Å
rg_real	49.66 Å
rg_real_error	2.35 Å
i0_real	1.3430e+09
i0_real_error	2.6830e+07
rg_reciprocal	49.29 Å
i0_reciprocal	1342000000.0000
total_estimate	0.7739
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	50.1 Å
skewness	0.454
kurtosis	-0.425
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	53180000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.728; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.871; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Menin
formula_weight	59790.0 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	15547

GSGLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVIPTNVPELTFQPSPAPDPPGGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKKVSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYHKGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEIYKEFFEVANDVIPNLLKEAASLLEAGSQGSALQDPECFAHLLRFYDGICKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSGTVAGTARGPEGGSTAQVPAPTASPPPEGPVLTFQSEKMKGMKELLVATKINSSAIKLQLTAQSQVQMKKQKVSTPSDYTLSFLKRQRKGL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	BETA-MERCAPTOETHANOL
formula_weight	78.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	;N-ethyl-5-fluoro-2-{[5-(2-{(3R)-6-[(2-methoxyethyl)(methyl)amino]-2-methylhexan-3-yl}-2,6-diazaspiro[3.4]octan-6-yl)-1,2,4-triazin-6-yl]oxy}-N-(propan-2-yl)benzamide ;
formula_weight	599.8 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	84

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6. Citations (1)

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length_a	143.372 Å
length_b	70.486 Å
length_c	145.561 Å
angle_alpha	90.00 °
angle_beta	91.68 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.950 Å
resolution_low	145.500 Å
r_factor	0.2366
r_work	0.2333
r_free	0.2969

fit	/app/data/saxs_computation/z4/9z4x/9z4x.fit
pddf	/app/data/pr_computation/z4/9z4x/9z4x.pr.out
profile	/app/data/saxs_computation/z4/9z4x/9z4x.dat

MENIN IN COMPLEX WITH JNJ-75276617 (Bleximenib)

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