6P7I

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein arginine N-methyltransferase 6A, B, C, D376Homo sapiensMutation(s): 1 
Gene Names: PRMT6HRMT1L6
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LA8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
M [auth D]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
O3S (Subject of Investigation/LOI)
Query on O3S

Download Ideal Coordinates CCD File 
N [auth D]N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]propanamide
C17 H24 N4 O
ZXTYIIDDTFQCGV-UHFFFAOYSA-N
 Ligand Interaction
O3P
Query on O3P

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
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 = 78.091α = 90
b = 135.133β = 98.01
c = 83.206γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing
HKL-3000data reduction
HKL-3000data collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references, Refinement description