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9q8g

Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 4 / EP102

Method: X-RAY DIFFRACTION D_max: 91.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q8g
deposition_date	2025-02-24
title	Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 4 / EP102
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	25.07 Å
rg_electron	24.51 Å
i0	92973200.00
molecular_weight	50646.0 kDa
excluded_volume	48986 Å³
envelope_volume	81895 Å³
shell_volume	28259 Å³
envelope_diameter	95.8 Å
shell_rg	31.50 Å
envelope_rg	24.83 Å
shape_rg	24.51 Å
total_rg	25.08 Å
total_atoms	3837
n_residues	465
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	91.2 Å
rg_real	25.13 Å
rg_real_error	0.73 Å
i0_real	9.2970e+07
i0_real_error	1.2370e+06
rg_reciprocal	25.11 Å
i0_reciprocal	92970000.0000
total_estimate	0.8273
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.5 Å
skewness	0.496
kurtosis	-0.059
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	20460000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.640; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.834; Smooth: 0.998

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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	24543.2 kDa
ec_number	2.1.1.348
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4145

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	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-[5-(5-cyclopropylpyridin-3-yl)-1,3,4-thiadiazol-2-yl]oxetan-3-yl]pyridin-3-yl]piperidin-3-amine ;
formula_weight	488.6 kDa
src_method	nat
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	266

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6. Citations (1)

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length_a	64.189 Å
length_b	64.189 Å
length_c	225.252 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	1.750 Å
resolution_low	49.900 Å
r_factor	0.2040
r_work	0.2018
r_free	0.2450

fit	/app/data/saxs_computation/q8/9q8g/9q8g.fit
pddf	/app/data/pr_computation/q8/9q8g/9q8g.pr.out
profile	/app/data/saxs_computation/q8/9q8g/9q8g.dat

Crystal structure of the human METTL3-METTL14 in complex with small molecule inhibitor Compound 4 / EP102

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)