7T39 | pdb_00007t39

Co-crystal structure of human PRMT9 in complex with MT221 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7T39/pdb

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


• Deposited: 2021-12-07 Released: 2021-12-22 
• Deposition Author(s): Zeng, H., Dong, A., Hutchinson, A., Seitova, A., Li, Y., Gao, Y.D., Schneider, S., Siliphaivanh, P., Sloman, D., Nicholson, B., Fischer, C., Hicks, J., Brown, P.J., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
• Funding Organization(s): The Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.269 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Co-crystal structure of human PRMT9 in complex with MT221 inhibitor

Zeng, H., Dong, A., Hutchinson, A., Seitova, A., Li, Y., Gao, Y.D., Schneider, S., Siliphaivanh, P., Sloman, D., Nicholson, B., Fischer, C., Hicks, J., Brown, P.J., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 80.96 kDa 
• Atom Count: 4,657 
• Modeled Residue Count: 613 
• Deposited Residue Count: 720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 9	A	720	Homo sapiens	Mutation(s): 0  Gene Names: PRMT9, PRMT10 EC: 2.1.1.320
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P2P2 (Homo sapiens) Explore Q6P2P2  Go to UniProtKB:  Q6P2P2
PHAROS:  Q6P2P2 GTEx:  ENSG00000164169

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EJB (Subject of Investigation/LOI)	B [auth A]	7-[5-S-(4-{[(2-ethylpyridin-3-yl)methyl]amino}butyl)-5-thio-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine C23 H32 N6 O3 S SBQBBUZLJIAJBR-GLHSZLCASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.269 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.138	α = 90
b = 82.735	β = 97.94
c = 65.836	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Zeng, H., Dong, A., Hutchinson, A., Seitova, A., Li, Y., Gao, Y.D., Schneider, S., Siliphaivanh, P., Sloman, D., Nicholson, B., Fischer, C., Hicks, J., Brown, P.J., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
The Structural Genomics Consortium (SGC)	Canada	--

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description