SMTL ID : 6p7i.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 22 residues within 4Å: Chain A: Y.48, Y.49, Y.52, H.58, M.61, R.67, G.91, A.92, G.93, I.96, L.97, E.113, A.114, S.115, G.139, P.140, V.141, E.142, E.156, M.167, S.170 Ligands: O3P.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.49, A:G.91, A:G.93, A:A.114, A:V.141, A:E.142, A:S.170 Water bridges: A:R.352 Salt bridges: A:R.67 pi-Stacking: A:Y.49, A:Y.49 SAH.4: 22 residues within 4Å: Chain B: Y.48, Y.49, Y.52, H.58, M.61, R.67, G.91, A.92, G.93, I.96, L.97, E.113, A.114, S.115, G.139, P.140, V.141, E.142, E.156, M.167, S.170 Ligands: O3P.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.49, B:G.91, B:G.93, B:A.114, B:V.141, B:E.142, B:S.170 Water bridges: B:R.352, B:R.352 Salt bridges: B:R.67 pi-Stacking: B:Y.49, B:Y.49

2 x O3P: N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]prop-2-enamide(Non-covalent)

O3P.2: 14 residues within 4Å: Chain A: Y.48, C.51, Y.52, V.57, E.60, M.61, E.156, W.157, M.158, Y.160, E.165, H.318, W.319 Ligands: SAH.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.48, A:Y.52, A:V.57, A:Y.160 Hydrogen bonds: A:Y.52, A:E.60, A:E.156 Salt bridges: A:E.156, A:E.165 O3P.5: 14 residues within 4Å: Chain B: Y.48, C.51, Y.52, V.57, E.60, M.61, E.156, W.157, M.158, Y.160, E.165, H.318, W.319 Ligands: SAH.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.57, B:Y.160 Hydrogen bonds: B:Y.52, B:Y.52, B:E.60, B:M.158 Salt bridges: B:E.156, B:E.165

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: A.255, Q.256, R.261, V.272, G.273 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.256, A:Q.256, A:G.273, A:G.273 Water bridges: A:R.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, Y. et al., Discovery of a First-in-Class Protein Arginine Methyltransferase 6 (PRMT6) Covalent Inhibitor. J.Med.Chem. (2020)

Release Date

2019-06-26

Peptides

Protein arginine N-methyltransferase 6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Protein arginine N-methyltransferase 6

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