← Back to search

9qsm

small molecule inhibitor in complex with PD-L1

Method: X-RAY DIFFRACTION D_max: 104.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qsm
deposition_date	2025-04-05
title	small molecule inhibitor in complex with PD-L1
keywords	PD-L1, small molecule inhibitors, immune checkpoint, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	32.52 Å
rg_electron	32.07 Å
i0	197250000.00
molecular_weight	75620.0 kDa
excluded_volume	73551 Å³
envelope_volume	137800 Å³
shell_volume	37054 Å³
envelope_diameter	109.7 Å
shell_rg	37.76 Å
envelope_rg	31.79 Å
shape_rg	32.07 Å
total_rg	32.43 Å
total_atoms	5721
n_residues	702
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	104.9 Å
rg_real	32.43 Å
rg_real_error	0.65 Å
i0_real	1.9730e+08
i0_real_error	2.9960e+06
rg_reciprocal	32.47 Å
i0_reciprocal	197300000.0000
total_estimate	0.8975
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.0 Å
skewness	0.177
kurtosis	-0.485
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0001
highest_alpha	16590000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.927

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Programmed cell death 1 ligand 1
formula_weight	14678.8 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	5806

AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHHHHHH

Source

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

Entity 2 non-polymer

description	;~{N}-[2-chloranyl-3-[2-chloranyl-3-[4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-3-methoxy-phenyl]phenyl]phenyl]-5-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]pyridine-2-carboxamide ;
formula_weight	715.6 kDa
src_method	syn
entity_count	3

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	85

▶

6. Citations (1)

▶

length_a	67.521 Å
length_b	74.996 Å
length_c	74.614 Å
angle_alpha	90.00 °
angle_beta	95.49 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.750 Å
resolution_low	47.620 Å
r_factor	—
r_work	0.2443
r_free	0.2702

fit	/app/data/saxs_computation/qs/9qsm/9qsm.fit
pddf	/app/data/pr_computation/qs/9qsm/9qsm.pr.out
profile	/app/data/saxs_computation/qs/9qsm/9qsm.dat

small molecule inhibitor in complex with PD-L1

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