SMTL ID : 5egs.2 (1 other biounit)

Human PRMT6 with bound fragment-type inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 23 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, V.112, E.113, A.114, S.115, G.139, P.140, V.141, E.142, E.156, M.167, S.170 Ligands: 5NR.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.49, A:G.91, A:G.91, A:G.93, A:A.114, A:S.115, A:V.141, A:E.142, A:S.170 Water bridges: A:E.156, A:R.352, A:R.352 Salt bridges: A:R.67 pi-Stacking: A:Y.49 SAH.3: 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: 5NR.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.49, B:G.91, B:A.114, B:V.141, B:E.142, B:S.170 Water bridges: B:E.156, B:R.352, B:R.352 Salt bridges: B:R.67 pi-Stacking: B:Y.49, B:Y.49

3 x 5NR: 2-[4-(phenylmethyl)piperidin-1-yl]ethanamine(Non-covalent)

5NR.2: 11 residues within 4Å: Chain A: C.51, Y.52, V.57, M.61, E.156, M.158, Y.160, E.165, H.318, W.319 Ligands: SAH.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.52, A:V.57, A:Y.160, A:Y.160 Hydrogen bonds: A:E.156 Salt bridges: A:E.156, A:E.165 5NR.4: 12 residues within 4Å: Chain B: C.51, Y.52, V.57, M.61, E.156, W.157, M.158, Y.160, E.165, H.318, W.319 Ligands: SAH.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.52, B:V.57, B:Y.160 Hydrogen bonds: B:Y.52, B:M.158 Salt bridges: B:E.156, B:E.165 5NR.5: 10 residues within 4Å: Chain B: L.163, S.166, S.169, E.265, L.268, E.269, L.344, L.345, P.346, L.354 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.163, B:L.163, B:L.268, B:L.354 Salt bridges: B:E.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferreira de Freitas, R. et al., Discovery of a Potent Class I Protein Arginine Methyltransferase Fragment Inhibitor. J.Med.Chem. (2016)

Release Date

2016-02-03

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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