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9q89

Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 13

Method: X-RAY DIFFRACTION D_max: 91.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q89
deposition_date	2025-02-24
title	Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 13
keywords	METTL3 METTL14 inhibitor, Epics, RNA BINDING PROTEIN; RNA BINDING 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	25.11 Å
rg_electron	24.54 Å
i0	93192200.00
molecular_weight	50787.0 kDa
excluded_volume	49169 Å³
envelope_volume	82217 Å³
shell_volume	28313 Å³
envelope_diameter	97.0 Å
shell_rg	31.47 Å
envelope_rg	24.93 Å
shape_rg	24.55 Å
total_rg	25.11 Å
total_atoms	3841
n_residues	466
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	91.4 Å
rg_real	25.16 Å
rg_real_error	0.93 Å
i0_real	9.3190e+07
i0_real_error	1.3560e+06
rg_reciprocal	25.15 Å
i0_reciprocal	93190000.0000
total_estimate	0.7500
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	27.6 Å
skewness	0.498
kurtosis	-0.053
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	20560000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.638; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.833; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	N6-adenosine-methyltransferase catalytic subunit
formula_weight	24527.2 kDa
ec_number	2.1.1.348
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4172

ADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	N(6)-adenosine-methyltransferase non-catalytic subunit METTL14
formula_weight	32550.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

HNDYCQHFVDTGHRPQNFIRDVGLADRFEEYPKLRELIRLKDELIAKSNTPPMYLQADIEAFDIRELTPKFDVILLEPPLEEYYRETGITANEKCWTWDDIMKLEIDEIAAPRSFIFLWCGSGEGLDLGRVCLRKWGYRRCEDICWIKTNKNNPGKTKTLDPKAVFQRTKEHCLMGIKGTVKRSTDGDFIHANVDIDLIITEEPEIGNIEKPVEIFHIIEHFCLGRRRLHLFGRDSTIRPGWLTVGPTLTNSNYNAETYASYFSAPNSYLTGCTEEIERL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 non-polymer

description	;(3~{R})-~{N}-(cyclopropylmethyl)-1-[6-[3-[4-(6-pyrrolidin-1-ylpyrazin-2-yl)-1,2,3-triazol-1-yl]oxetan-3-yl]pyridin-3-yl]piperidin-3-amine ;
formula_weight	501.6 kDa
src_method	nat
entity_count	1

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	246

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6. Citations (1)

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length_a	64.533 Å
length_b	64.533 Å
length_c	226.609 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	1.950 Å
resolution_low	44.930 Å
r_factor	0.1923
r_work	0.1899
r_free	0.2379

fit	/app/data/saxs_computation/q8/9q89/9q89.fit
pddf	/app/data/pr_computation/q8/9q89/9q89.pr.out
profile	/app/data/saxs_computation/q8/9q89/9q89.dat

Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 13

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)