9AY9 | pdb_00009ay9

Co-crystal structure of human PRMT9 in complex with MRK-990 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9AY9/pdb

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


• Deposited: 2024-03-07 Released: 2024-12-04 
• Deposition Author(s): Zeng, H., Dong, A., Li, Y., 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): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.235 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Co-crystal structure of human PRMT9 in complex with MRK-990 inhibitor

Zeng, H., Dong, A., Li, Y., 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 324 kDa 
• Atom Count: 19,473 
• Modeled Residue Count: 2,472 
• Deposited Residue Count: 2,880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 9	A, B, C, D	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AHM (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], I [auth D]	7-[5-S-(4-{[(2-tert-butylpyridin-3-yl)methyl]amino}butyl)-5-thio-beta-D-ribofuranosyl]-5-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine C26 H38 N6 O3 S PLCITURFVJNAFH-GUQHISFFSA-N
UNX	H [auth C], J [auth D]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.235 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.374	α = 90
b = 223.078	β = 90.23
c = 84.698	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Zeng, H., Dong, A., Li, Y., 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
Other private		--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release