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9vcz

The crystal structure of BRD4-BD1 in complex with inhibitor 39b

Method: X-RAY DIFFRACTION D_max: 54.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vcz
deposition_date	2025-06-07
last_revision	2026-06-10
title	The crystal structure of BRD4-BD1 in complex with inhibitor 39b
keywords	BRD4, BD1, inhibitor, STRUCTURAL PROTEIN; STRUCTURAL 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	16.18 Å
rg_electron	14.94 Å
i0	4430530.00
molecular_weight	15633.0 kDa
excluded_volume	19774 Å³
envelope_volume	21973 Å³
shell_volume	12647 Å³
envelope_diameter	52.6 Å
shell_rg	20.45 Å
envelope_rg	15.40 Å
shape_rg	14.91 Å
total_rg	16.11 Å
total_atoms	2171
n_residues	126
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	54.9 Å
rg_real	16.13 Å
rg_real_error	0.34 Å
i0_real	4.4310e+06
i0_real_error	5.1110e+04
rg_reciprocal	16.13 Å
i0_reciprocal	4431000.0000
total_estimate	0.8733
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	19.0 Å
skewness	0.279
kurtosis	-0.299
angular_range	— – 0.4900 Å⁻¹
current_alpha	0.0000
highest_alpha	1052000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.987

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Bromodomain-containing protein 4
formula_weight	15012.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2335

MNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

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

Entity 3 non-polymer

description	1-[3-chloranyl-4-[(2-methyl-3-oxidanylidene-cyclopenten-1-yl)amino]phenyl]-3-(4-methoxyphenyl)urea
formula_weight	385.8 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	146

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6. Citations (1)

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length_a	37.667 Å
length_b	43.829 Å
length_c	77.674 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	1.500 Å
resolution_low	38.840 Å
r_factor	0.1764
r_work	0.1743
r_free	0.1965

fit	/app/data/saxs_computation/vc/9vcz/9vcz.fit
pddf	/app/data/pr_computation/vc/9vcz/9vcz.pr.out
profile	/app/data/saxs_computation/vc/9vcz/9vcz.dat