6WAD

Crystal Structure of Human Protein arginine N-methyltransferase 6 (PRMT6) in complex with MT2739 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6WAD/pdb

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


• Deposited: 2020-03-25 Released: 2020-09-02 
• Deposition Author(s): Halabelian, L., Zeng, H., Dong, A., Schapira, M., De Freitas, R.F., Hutchinson, A., Seitova, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

Crystal Structure of Human Protein arginine N-methyltransferase 6 (PRMT6) in complex with MT2739 inhibitor

Halabelian, L., Zeng, H., Dong, A., Schapira, M., De Freitas, R.F., Hutchinson, A., Seitova, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

To be published.

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)

Macromolecule Content

• Total Structure Weight: 42.85 kDa 
• Atom Count: 2,483 
• Modelled Residue Count: 321 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 6	A	376	Homo sapiens	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TQ7 (Subject of Investigation/LOI)	C [auth A]	5-bromo-N-(diphenylmethyl)-N-methylthiophene-2-carboxamide C19 H16 Br N O S WORZHUYQQIIZTA-UHFFFAOYSA-N
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.226 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.068	α = 90
b = 94.068	β = 90
c = 109.242	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-02 
Deposition Author(s): Halabelian, L., Zeng, H., Dong, A., Schapira, M., De Freitas, R.F., Hutchinson, A., Seitova, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Brown, P.J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2020-09-02
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Structure summary