9N3N | pdb_00009n3n

Crystal structure of PRMT5:MEP50 in complex with MTA and oxamide compound 3

PDB DOI: https://doi.org/10.2210/pdb9N3N/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2025-01-31 Released: 2025-03-12
Deposition Author(s): Whittington, D.A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.264 (Depositor), 0.264 (DCC)
R-Value Work:
0.218 (Depositor), 0.218 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of TNG462: A Highly Potent and Selective MTA-Cooperative PRMT5 Inhibitor to Target Cancers with MTAP Deletion.

Cottrell, K.M., Briggs, K.J., Tsai, A., Tonini, M.R., Whittington, D.A., Gong, S., Liang, C., McCarren, P., Zhang, M., Zhang, W., Huang, A., Maxwell, J.P.

(2025) J Med Chem 68: 5097-5119

PubMed: 40035511 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.4c03067
Primary Citation of Related Structures:
9N3N, 9N3O, 9N3P, 9N3Q, 9N3R

PubMed Abstract:
The gene encoding for MTAP is one of the most commonly deleted genes in cancer, occurring in approximately 10-15% of all human cancer. We have previously described the discovery of TNG908, a brain-penetrant clinical-stage compound that selectively targets MTAP -deleted cancer cells by binding to and inhibiting PRMT5 cooperatively with MTA, which is present in elevated concentrations in MTAP -deleted cells. Herein we describe the discovery of TNG462, a more potent and selective MTA-cooperative PRMT5 inhibitor with improved DMPK properties that is selective for MTAP -deleted cancers and is currently in Phase I/II clinical trials.

Organizational Affiliation

Tango Therapeutics, Boston, Massachusetts 02215, United States.

Macromolecule Content

Total Structure Weight: 113.84 kDa
Atom Count: 7,636
Modelled Residue Count: 927
Deposited Residue Count: 995
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 5	A	645	Homo sapiens	Mutation(s): 0 Gene Names: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 EC: 2.1.1.320
UniProt & NIH Common Fund Data Resources
Find proteins for O14744 (Homo sapiens) Explore O14744 Go to UniProtKB: O14744
PHAROS: O14744 GTEx: ENSG00000100462
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14744
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylosome protein 50	B	350	Homo sapiens	Mutation(s): 0 Gene Names: WDR77, MEP50, WD45, HKMT1069, Nbla10071
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQA1 (Homo sapiens) Explore Q9BQA1 Go to UniProtKB: Q9BQA1
PHAROS: Q9BQA1 GTEx: ENSG00000116455
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BQA1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BV5 (Subject of Investigation/LOI) Query on A1BV5 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	N-(6-amino-5-cyclopropylpyridin-3-yl)-2-[(2R,5S)-2-(1,3-benzothiazol-5-yl)-5-methylpiperidin-1-yl]-2-oxoacetamide C₂₃ H₂₅ N₅ O₂ S QNHCUYXLHQODAB-ORAYPTAESA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MTA Query on MTA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	5'-DEOXY-5'-METHYLTHIOADENOSINE C₁₁ H₁₅ N₅ O₃ S WUUGFSXJNOTRMR-IOSLPCCCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A] mmCIF format, chain W [auth A]	W [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain Z [auth B] SDF format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain U [auth A]	U [auth A], V [auth A], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Focus chain V [auth A] Focus chain Z [auth B] Interactions & Density Focus chain U [auth A] Focus chain V [auth A] Focus chain Z [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth A] SDF format, chain X [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain Y [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain X [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain X [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain Y [auth B]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], X [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain X [auth B] Focus chain Y [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]