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9q8a

Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 3

Method: X-RAY DIFFRACTION D_max: 93.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q8a
deposition_date	2025-02-24
title	Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 3
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	25.00 Å
rg_electron	24.48 Å
i0	90196700.00
molecular_weight	49974.0 kDa
excluded_volume	48394 Å³
envelope_volume	81052 Å³
shell_volume	28013 Å³
envelope_diameter	95.7 Å
shell_rg	31.37 Å
envelope_rg	24.88 Å
shape_rg	24.48 Å
total_rg	25.04 Å
total_atoms	3788
n_residues	459
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	93.2 Å
rg_real	25.08 Å
rg_real_error	0.75 Å
i0_real	9.0200e+07
i0_real_error	1.4480e+06
rg_reciprocal	25.06 Å
i0_reciprocal	90200000.0000
total_estimate	0.8125
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	28.1 Å
skewness	0.497
kurtosis	-0.060
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0001
highest_alpha	19780000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.595; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.775; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	N(6)-adenosine-methyltransferase catalytic subunit METTL3
formula_weight	24341.0 kDa
ec_number	2.1.1.348
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3970

RLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKP

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	32411.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

NDYCQHFVDTGHRPQNFIRDVGLADRFEEYPKLRELIRLKDELIAKSNTPPMYLQADIEAFDIRELTPKFDVILLEPPLEEYYRETGITANEKCWTWDDIMKLEIDEIAAPRSFIFLWCGSGEGLDLGRVCLRKWGYRRCEDICWIKTNKNNPGKTKTLDPKAVFQRTKEHCLMGIKGTVKRSTDGDFIHANVDIDLIITEEPEIGNIEKPVEIFHIIEHFCLGRRRLHLFGRDSTIRPGWLTVGPTLTNSNYNAETYASYFSAPNSYLTGCTEEIERL

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-(5-cyclopropylpyridin-3-yl)-1,2,3-triazol-1-yl]oxetan-3-yl]pyridin-3-yl]piperidin-3-amine ;
formula_weight	471.6 kDa
src_method	nat
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	162

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6. Citations (1)

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length_a	64.042 Å
length_b	64.042 Å
length_c	224.985 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	49.790 Å
r_factor	0.1961
r_work	0.1935
r_free	0.2447

fit	/app/data/saxs_computation/q8/9q8a/9q8a.fit
pddf	/app/data/pr_computation/q8/9q8a/9q8a.pr.out
profile	/app/data/saxs_computation/q8/9q8a/9q8a.dat

Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 3

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)