7S1Q | pdb_00007s1q

PRMT5/MEP50 crystal structure with MTA and a phthalazinone inhibitor bound (Compound 9)

• PDB DOI: https://doi.org/10.2210/pdb7S1Q/pdb

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


• Deposited: 2021-09-02 Released: 2022-01-26 
• Deposition Author(s): Gunn, R.J., Thomas, N.C., Lawson, J.D., Ivetac, A., Smith, C.R., Kulyk, S., Marx, M.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 
  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Fragment-Based Discovery of MRTX1719, a Synthetic Lethal Inhibitor of the PRMT5•MTA Complex for the Treatment of MTAP -Deleted Cancers.

Smith, C.R., Aranda, R., Bobinski, T.P., Briere, D.M., Burns, A.C., Christensen, J.G., Clarine, J., Engstrom, L.D., Gunn, R.J., Ivetac, A., Jean-Baptiste, R., Ketcham, J.M., Kobayashi, M., Kuehler, J., Kulyk, S., Lawson, J.D., Moya, K., Olson, P., Rahbaek, L., Thomas, N.C., Wang, X., Waters, L.M., Marx, M.A.

(2022) J Med Chem 65: 1749-1766

• PubMed: 35041419 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c01900
• Primary Citation Related Structures: 
  7S0U, 7S1P, 7S1Q, 7S1R, 7S1S, 7SER, 7SES


• PubMed Abstract: 
  

  The PRMT5•MTA complex has recently emerged as a new synthetically lethal drug target for the treatment of MTAP -deleted cancers. Here, we report the discovery of development candidate MRTX1719 . MRTX1719 is a potent and selective binder to the PRMT5•MTA complex and selectively inhibits PRMT5 activity in MTAP -deleted cells compared to MTAP -wild-type cells. Daily oral administration of MRTX1719 to tumor xenograft-bearing mice demonstrated dose-dependent inhibition of PRMT5-dependent symmetric dimethylarginine protein modification in MTAP -deleted tumors that correlated with antitumor activity. A 4-(aminomethyl)phthalazin-1(2 H )-one hit was identified through a fragment-based screen, followed by X-ray crystallography, to confirm binding to the PRMT5•MTA complex. Fragment growth supported by structural insights from X-ray crystallography coupled with optimization of pharmacokinetic properties aided the discovery of development candidate MRTX1719 .

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Organizational Affiliation: 
• Mirati Therapeutics, San Diego, California 92121, United States.
DSG, San Diego, California 92130, United States.
ZoBio BV, J. H. Oortweg 19, 2333 CH Leiden, Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 112.18 kDa 
• Atom Count: 7,365 
• Modeled Residue Count: 922 
• Deposited Residue Count: 995 
• Unique protein chains: 2

Macromolecules

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 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTA	C [auth A]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
84W (Subject of Investigation/LOI)	D [auth A]	[7-(1-methyl-1H-pyrazol-4-yl)-4-oxo-3,4-dihydrophthalazin-1-yl]methanaminium C13 H14 N5 O HUDGQDMMFLDCAM-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free:  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.342	α = 90
b = 137.646	β = 90
c = 178.66	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-01-26 
Deposition Author(s): Gunn, R.J., Thomas, N.C., Lawson, J.D., Ivetac, A., Smith, C.R., Kulyk, S., Marx, M.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-01-26
  Type: Initial release
  
• Version 1.1: 2022-02-02
  Changes: Database references, Structure summary
• Version 1.2: 2022-02-23
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description