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9veq

Crystal structure of Keap1 in complex with a small molecule inhibitor, KMN003

Method: X-RAY DIFFRACTION D_max: 93.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9veq
deposition_date	2025-06-10
title	Crystal structure of Keap1 in complex with a small molecule inhibitor, KMN003
keywords	Nrf2 inhibitor, PEPTIDE BINDING PROTEIN, PEPTIDE BINDING PROTEIN-INHIBITOR complex; PEPTIDE BINDING PROTEIN/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	28.21 Å
rg_electron	27.84 Å
i0	132385000.00
molecular_weight	59349.0 kDa
excluded_volume	56493 Å³
envelope_volume	93081 Å³
shell_volume	28610 Å³
envelope_diameter	99.8 Å
shell_rg	34.11 Å
envelope_rg	27.86 Å
shape_rg	27.82 Å
total_rg	28.32 Å
total_atoms	4468
n_residues	570
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	93.4 Å
rg_real	28.39 Å
rg_real_error	0.77 Å
i0_real	1.3240e+08
i0_real_error	2.1540e+06
rg_reciprocal	28.33 Å
i0_reciprocal	132400000.0000
total_estimate	0.8549
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.7 Å
skewness	0.444
kurtosis	-0.523
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	20170000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.863; Smooth: 0.954

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Kelch-like ECH-associated protein 1
formula_weight	31652.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4987

GAPKVGRLIYTAGGYFRQSLSYLEAYNPSNGSWLRLADLQVPRSGLAGCVVGGLLYAVGGRNNSPDGNTDSSALDCYNPMTNQWSPCASMSVPRNRIGVGVIDGHIYAVGGSHGCIHHSSVERYEPERDEWHLVAPMLTRRIGVGVAVLNRLLYAVGGFDGTNRLNSAECYYPERNEWRMITPMNTIRSGAGVCVLHNCIYAAGGYDGQDQLNSVERYDVETETWTFVAPMRHHRSALGITVHQGKIYVLGGYDGHTFLDSVECYDPDSDTWSEVTRMTSGRSGVGVAVT

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 non-polymer

description	4-[1,4-bis[(4-ethoxyphenyl)sulfonylamino]naphthalen-2-yl]butanoic acid
formula_weight	612.7 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	FORMIC ACID
formula_weight	46.0 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	519

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6. Citations (1)

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length_a	125.810 Å
length_b	75.199 Å
length_c	110.368 Å
angle_alpha	90.00 °
angle_beta	105.10 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.700 Å
resolution_low	36.410 Å
r_factor	0.1826
r_work	0.1815
r_free	0.2050

fit	/app/data/saxs_computation/ve/9veq/9veq.fit
pddf	/app/data/pr_computation/ve/9veq/9veq.pr.out
profile	/app/data/saxs_computation/ve/9veq/9veq.dat

Crystal structure of Keap1 in complex with a small molecule inhibitor, KMN003

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