7UOH

PRMT5/MEP50 crystal structure with MTA and an achiral, class 1, non-atropisomeric inhibitor bound

• PDB DOI: https://doi.org/10.2210/pdb7UOH/pdb

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


• Deposited: 2022-04-12 Released: 2022-08-17 
• Deposition Author(s): Gunn, R.J., Thomas, N.C., Lawson, J.D., Ivetac, A., Kulyk, S., Smith, C.R., Marx, M.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.232 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Design and evaluation of achiral, non-atropisomeric 4-(aminomethyl)phthalazin-1(2H)-one derivatives as novel PRMT5/MTA inhibitors.

Smith, C.R., Aranda, R., Christensen, J.G., Engstrom, L.D., Gunn, R.J., Ivetac, A., Ketcham, J.M., Kuehler, J., David Lawson, J., Marx, M.A., Olson, P., Thomas, N.C., Wang, X., Waters, L.M., Kulyk, S.

(2022) Bioorg Med Chem 71: 116947-116947

• PubMed: 35926325 
• DOI: https://doi.org/10.1016/j.bmc.2022.116947
• Primary Citation of Related Structures:  
  7UOH


• PubMed Abstract: 
  

  MRTX1719 is an inhibitor of the PRMT5/MTA complex and recently entered clinical trials for the treatment of MTAP-deleted cancers. MRTX1719 is a class 3 atropisomeric compound that requires a chiral synthesis or a chiral separation step in its preparation. Here, we report the SAR and medicinal chemistry design strategy, supported by structural insights from X-ray crystallography, to discover a class 1 atropisomeric compound from the same series that does not require a chiral synthesis or a chiral separation step in its preparation.

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Organizational Affiliation: 

Mirati Therapeutics, San Diego, CA 92121, United States. Electronic address: [e-mail].

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: 112.41 kDa 
• Atom Count: 7,405 
• Modelled Residue Count: 927 
• 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
NXF (Subject of Investigation/LOI)	C [auth A]	(2M)-2-[(4M)-4-{4-(aminomethyl)-1-oxo-8-[(2R)-oxolan-2-yl]-1,2-dihydrophthalazin-6-yl}-1-methyl-1H-pyrazol-5-yl]-1-benzothiophene-3-carbonitrile C26 H22 N6 O2 S RXOUGZIIVASWRH-OAQYLSRUSA-N
MTA	D [auth A]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MTA	BindingDB:  7UOH	Kd: 661 (nM) from 1 assay(s)
NXF	BindingDB:  7UOH	IC50: min: 4, max: 174 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.232 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.638	α = 90
b = 138.1	β = 90
c = 179.319	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-17 
Deposition Author(s): Gunn, R.J., Thomas, N.C., Lawson, J.D., Ivetac, A., Kulyk, S., Smith, C.R., Marx, M.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-08-17
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description