7OEM

Crystal structure of the human METTL3-METTL14 complex with compound UOZ120

PDB DOI: https://doi.org/10.2210/pdb7OEM/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2021-05-03 Released: 2021-10-20
Deposition Author(s): Bedi, R.K., Huang, D., Caflisch, A.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.258
R-Value Work: 0.207
R-Value Observed: 0.209

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure-Based Design of Inhibitors of the m6A-RNA Writer Enzyme METTL3

Bedi, R.K., Huang, D., Li, Y., Caflisch, A.

(2023) ACS Bio Med Chem Au

DOI: https://doi.org/10.1021/acsbiomedchemau.3c00023

Macromolecule Content

Total Structure Weight: 62.51 kDa
Atom Count: 3,640
Modelled Residue Count: 441
Deposited Residue Count: 536
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N6-adenosine-methyltransferase catalytic subunit	A	246	Homo sapiens	Mutation(s): 0 Gene Names: METTL3, MTA70 EC: 2.1.1.348
UniProt & NIH Common Fund Data Resources
Find proteins for Q86U44 (Homo sapiens) Explore Q86U44 Go to UniProtKB: Q86U44
PHAROS: Q86U44 GTEx: ENSG00000165819
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86U44
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N6-adenosine-methyltransferase non-catalytic subunit	B	290	Homo sapiens	Mutation(s): 0 Gene Names: METTL14, KIAA1627
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCE5 (Homo sapiens) Explore Q9HCE5 Go to UniProtKB: Q9HCE5
PHAROS: Q9HCE5 GTEx: ENSG00000145388
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HCE5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VB8 (Subject of Investigation/LOI) Query on VB8 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	4-[(4,4-dimethylpiperidin-1-yl)methyl]-2-methylsulfanyl-~{N}-[[(3~{R})-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-yl]methyl]benzamide C₃₃ H₄₄ N₆ O₂ S CGGPQJWTZLKAFY-MGBGTMOVSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	C [auth A], D [auth A], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]