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9ysi

Covalent allosteric inhibitor of human DNA polymerase theta

Method: X-RAY DIFFRACTION D_max: 148.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ysi
deposition_date	2025-10-18
last_revision	2026-05-20
title	Covalent allosteric inhibitor of human DNA polymerase theta
keywords	inhibitor, complex, DNA BINDING PROTEIN, DNA-TRANSFERASE-INHIBITOR complex; DNA/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	42.68 Å
rg_electron	42.88 Å
i0	782932000.00
molecular_weight	147810.0 kDa
excluded_volume	140000 Å³
envelope_volume	263190 Å³
shell_volume	53205 Å³
envelope_diameter	149.3 Å
shell_rg	45.43 Å
envelope_rg	42.43 Å
shape_rg	42.90 Å
total_rg	42.95 Å
total_atoms	11070
n_residues	1349
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	148.4 Å
rg_real	42.95 Å
rg_real_error	1.39 Å
i0_real	7.8290e+08
i0_real_error	1.3330e+07
rg_reciprocal	42.68 Å
i0_reciprocal	782700000.0000
total_estimate	0.8416
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.1 Å
skewness	0.476
kurtosis	-0.454
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	60650000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.814

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	DNA polymerase theta
formula_weight	75200.1 kDa
ec_number	2.7.7.7
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	11962

GASSSSESLSIIDVASDQNLFQTFIKEWRCKKRFSISLACEKIRSLTSSKTGFPIKGCDDTLVVGLAVCWGGRDAYYFSLQKESLDPSLTLKDRMWYLQSCLRKESDKECSVVIYDFIQSYKILLLSCGISLEQSYEDPKVACWLLDPDSQEPTLHSIVTSFLPHELPLLEGMETSQGIQSLGLNAGSEHSGRYRASVESILIFNSMNQLNSLLQKENLQDVFRKVEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLDAIETQAYQLAGHSFSFTSSDDIAEVLFLELKLPPNRELGRQFSTSKDVLNKLKALHPLPGLILEWRRITNAITKVVFPLQREKCLNPFLGMERIYPVSQSHTATGRITFTEPNIQNVPRDFEIKMPTLADRGMPFSISMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLETFHSTFKSHGHREGMLQSDQTGGMFCPIRGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKLSVKLKVKVKIGASWGELKDFDV

Source

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

Entity 2 polymer

description	;DNA (5'-D(CPGPTPCPCPAPAPTPGPAPCPAPGPCP*C)-3') ;
formula_weight	5157.4 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	B,E

CGTCCAATGACAGCCGC

Entity 3 polymer

description	;DNA (5'-D(GPGPCPTPGPTPCPAPTPTP*G)-3') ;
formula_weight	3998.6 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	C,F

GCGGCTGTCATTG

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
formula_weight	491.2 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 8 non-polymer

description	N-(4-{2-[2,4-bis(trifluoromethyl)phenyl]-N-phenylacetamido}but-2-yn-1-yl)-2-(ethanesulfonamido)benzamide
formula_weight	625.6 kDa
src_method	syn
entity_count	2

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	892

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6. Citations (2)

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length_a	248.522 Å
length_b	66.621 Å
length_c	151.914 Å
angle_alpha	90.00 °
angle_beta	122.23 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.000 Å
resolution_low	60.970 Å
r_factor	0.1772
r_work	0.1754
r_free	0.2107

fit	/app/data/saxs_computation/ys/9ysi/9ysi.fit
pddf	/app/data/pr_computation/ys/9ysi/9ysi.pr.out
profile	/app/data/saxs_computation/ys/9ysi/9ysi.dat

Covalent allosteric inhibitor of human DNA polymerase theta

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

5. Entities & Polymer Info (9)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)