SMTL ID : 4y2h.1

Crystal structure of human protein arginine methyltransferase PRMT6 bound to SAH and an aryl pyrazole inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 22 residues within 4Å: Chain A: Y.24, Y.25, Y.28, H.34, M.37, R.43, G.67, A.68, G.69, I.72, L.73, E.89, A.90, S.91, G.115, P.116, V.117, E.118, E.132, M.143, S.146 Ligands: 49K.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.67, A:G.69, A:A.90, A:V.117, A:E.118, A:S.146 Water bridges: A:R.328 Salt bridges: A:R.43 pi-Stacking: A:Y.25 SAH.3: 22 residues within 4Å: Chain B: Y.24, Y.25, Y.28, H.34, M.37, R.43, G.67, A.68, G.69, I.72, L.73, E.89, A.90, S.91, G.115, P.116, V.117, E.118, E.132, M.143, S.146 Ligands: 49K.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.67, B:G.69, B:A.90, B:V.117, B:E.118, B:S.146 Water bridges: B:H.34, B:R.328 Salt bridges: B:R.43 pi-Stacking: B:Y.25

2 x 49K: N-{[5-(4-fluorophenyl)-1H-pyrazol-4-yl]methyl}-N-methylethane-1,2-diamine(Non-covalent)

49K.2: 12 residues within 4Å: Chain A: Y.28, V.33, E.36, M.37, E.132, W.133, M.134, Y.136, E.141, H.294, W.295 Ligands: SAH.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.28, A:V.33, A:Y.136 Hydrogen bonds: A:E.132 Water bridges: A:Y.28 Salt bridges: A:E.132, A:E.141 49K.4: 12 residues within 4Å: Chain B: Y.28, V.33, E.36, M.37, E.132, M.134, Y.136, H.140, E.141, H.294, W.295 Ligands: SAH.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.28, B:Y.28, B:Y.136 Hydrogen bonds: B:M.134 Water bridges: B:Y.28 Salt bridges: B:E.132, B:E.141

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain B: L.139, S.142, L.244, L.321, P.322, P.327, R.328, R.329, L.330 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.141, B:S.142, B:L.244, B:R.329 Water bridges: B:L.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mitchell, L.H. et al., Aryl Pyrazoles as Potent Inhibitors of Arginine Methyltransferases: Identification of the First PRMT6 Tool Compound. Acs Med.Chem.Lett. (2015)

Release Date

2015-04-22

Peptides

Protein arginine N-methyltransferase 6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein arginine N-methyltransferase 6