8CTB | pdb_00008ctb

Human PRMT5:MEP50 structure with Fragment 3 and MTA Bound

• PDB DOI: https://doi.org/10.2210/pdb8CTB/pdb

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


• Deposited: 2022-05-13 Released: 2022-10-05 
• Deposition Author(s): Gunn, R.J., Lawson, J.D., Smith, C.R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.288 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Fragment optimization and elaboration strategies - the discovery of two lead series of PRMT5/MTA inhibitors from five fragment hits.

Smith, C.R., Kulyk, S., Ahmad, M.U.D., Arkhipova, V., Christensen, J.G., Gunn, R.J., Ivetac, A., Ketcham, J.M., Kuehler, J., Lawson, J.D., Thomas, N.C., Wang, X., Marx, M.A.

(2022) RSC Med Chem 13: 1549-1564

• PubMed: 36545438 
• DOI: https://doi.org/10.1039/d2md00163b
• Primary Citation Related Structures: 
  7UY1, 7UYF, 7ZUP, 7ZUQ, 7ZUU, 7ZUY, 7ZV2, 7ZVL, 7ZVU, 8CSG, 8CTB


• PubMed Abstract: 
  

  Here we describe the early stages of a fragment-based lead discovery (FBLD) project for a recently elucidated synthetic lethal target, the PRMT5/MTA complex, for the treatment of MTAP -deleted cancers. Starting with five fragment/PRMT5/MTA X-ray co-crystal structures, we employed a two-phase fragment elaboration process encompassing optimization of fragment hits and subsequent fragment growth to increase potency, assess synthetic tractability, and enable structure-based drug design. Two lead series were identified, one of which led to the discovery of the clinical candidate MRTX1719.

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Organizational Affiliation: 
• Mirati Therapeutics San Diego California 92121 USA [e-mail] [e-mail].
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: 112.1 kDa 
• Atom Count: 7,389 
• Modeled Residue Count: 924 
• 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 (Subject of Investigation/LOI)	D [auth A]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
PWX (Subject of Investigation/LOI)	C [auth A]	7-chloro-1-methyl-1H-benzimidazol-2-amine C8 H8 Cl N3 SXLPXHZFEJYXBB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PWX	BindingDB:  8CTB	Kd: 1.20e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.288 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.983	α = 90
b = 137.232	β = 90
c = 178.304	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: 2022-10-05 
Deposition Author(s): Gunn, R.J., Lawson, J.D., Smith, C.R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-10-05
  Type: Initial release
  
• Version 1.1: 2023-01-11
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description