7U30 | pdb_00007u30

PRMT5:MEP50 Complexed with Cyclonucleoside Compound 1

PDB DOI: https://doi.org/10.2210/pdb7U30/pdb

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

Deposited: 2022-02-25 Released: 2022-06-01
Deposition Author(s): Palte, R.L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.208 (Depositor), 0.218 (DCC)
R-Value Work:
0.210 (Depositor), 0.220 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Design and synthesis of unprecedented 9- and 10-membered cyclonucleosides with PRMT5 inhibitory activity.

Kawamura, S., Palte, R.L., Kim, H.Y., Sauri, J., Sondey, C., Mansueto, M.S., Altman, M.D., Machacek, M.R.

(2022) Bioorg Med Chem 66: 116820-116820

PubMed: 35594650 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2022.116820
Primary Citation Related Structures:
7U30

PubMed Abstract:
Synthesis of medium-sized rings is known to be challenging due to high transannular strain especially for 9- and 10-membered rings. Herein we report design and synthesis of unprecedented 9- and 10-membered purine 8,5'-cyclonucleosides as the first cyclonucleoside PRMT5 inhibitors. The cocrystal structure of PRMT5:MEP50 in complex with the synthesized 9-membered cyclonucleoside 1 revealed its binding mode in the SAM binding pocket of PRMT5.

Organizational Affiliation

Discovery Chemistry, Merck & Co., Inc., Boston, MA 02115, United States. Electronic address: shuhei.kawamura@merck.com.

Macromolecule Content

Total Structure Weight: 109.46 kDa
Atom Count: 7,578
Modeled Residue Count: 936
Deposited Residue Count: 970
Unique protein chains: 2

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14744
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylosome protein 50	B	325	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BQA1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LB3 (Subject of Investigation/LOI) Query on LB3 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	(9R,10R,11S,12R,13R,14R)-4-amino-9-(3,4-difluorophenyl)-6,7,8,9,10,11,12,13-octahydro-10,13-epoxy[1,3]diazecino[1,2-e]purine-11,12-diol C₁₈ H₁₈ F₂ N₆ O₃ JZKFSFVCJQMNFZ-TXXSDKCWSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B]