6P7I

Crystal structure of Human PRMT6 in complex with S-Adenosyl-L-Homocysteine and YS17-117 Compound

• PDB DOI: https://doi.org/10.2210/pdb6P7I/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2019-06-05 Released: 2019-06-26 
• Deposition Author(s): Halabelian, L., Dong, A., Zeng, H., Li, Y., Seitova, A., Hutchinson, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.222 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Discovery of a First-in-Class Protein Arginine Methyltransferase 6 (PRMT6) Covalent Inhibitor

Shen, Y., Li, F., Szewczyk, M.M., Halabelian, L., Park, K.S., Chau, I., Dong, A., Zeng, H., Chen, H., Meng, F., Barsyte-Lovejoy, D., Arrowsmith, C.H., Brown, P.J., Liu, J., Vedadi, M., Jin, J.

(2020) J Med Chem 63: 5477-5487

• DOI: https://doi.org/10.1021/acs.jmedchem.0c00406

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 171.22 kDa 
• Atom Count: 11,633 
• Modelled Residue Count: 1,351 
• Deposited Residue Count: 1,504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 6	A, B, C, D	376	Homo sapiens	Mutation(s): 1  Gene Names: PRMT6, HRMT1L6 EC: 2.1.1.319
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LA8 (Homo sapiens) Explore Q96LA8  Go to UniProtKB:  Q96LA8
PHAROS:  Q96LA8 GTEx:  ENSG00000198890

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	E [auth A], H [auth B], K [auth C], M [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
O3S (Subject of Investigation/LOI)	N [auth D]	N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]propanamide C17 H24 N4 O ZXTYIIDDTFQCGV-UHFFFAOYSA-N
O3P	F [auth A], I [auth B], L [auth C]	N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]prop-2-enamide C17 H22 N4 O HVDMIAFOVVMNJF-UHFFFAOYSA-N
GOL	G [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
O3P	BindingDB:  6P7I	Ki: 16 (nM) from 1 assay(s)
		IC50: min: 18, max: 1300 (nM) from 2 assay(s)
O3S	BindingDB:  6P7I	IC50: 28 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.222 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.091	α = 90
b = 135.133	β = 98.01
c = 83.206	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing
HKL-3000	data reduction
HKL-3000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Halabelian, L., Dong, A., Zeng, H., Li, Y., Seitova, A., Hutchinson, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2022-02-23
  Changes: Database references, Refinement description
• Version 1.2: 2023-10-11
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-09
  Changes: Data collection, Structure summary