SMTL ID : 4y30.1

Crystal structure of human protein arginine methyltransferase PRMT6 bound to SAH and EPZ020411

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 23 residues within 4Å: Chain A: Y.23, Y.24, Y.27, H.33, M.36, R.42, G.66, A.67, G.68, I.71, L.72, V.87, E.88, A.89, S.90, G.114, P.115, V.116, E.117, E.131, M.142, S.145 Ligands: 49L.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.66, A:G.68, A:A.89, A:V.116, A:E.117, A:S.145 Water bridges: A:R.327, A:R.327 Salt bridges: A:R.42 pi-Stacking: A:Y.24 SAH.6: 23 residues within 4Å: Chain B: Y.23, Y.24, Y.27, H.33, M.36, R.42, G.66, A.67, G.68, I.71, L.72, V.87, E.88, A.89, S.90, G.114, P.115, V.116, E.117, E.131, M.142, S.145 Ligands: 49L.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.66, B:G.68, B:A.89, B:V.116, B:E.117, B:S.145 Water bridges: B:E.131, B:R.327 Salt bridges: B:R.42 pi-Stacking: B:Y.24, B:Y.24

2 x 49L: N,N'-dimethyl-N-({3-[4-({trans-3-[2-(tetrahydro-2H-pyran-4-yl)ethoxy]cyclobutyl}oxy)phenyl]-1H-pyrazol-4-yl}methyl)ethane-1,2-diamine(Non-covalent)

49L.2: 16 residues within 4Å: Chain A: L.22, Y.23, Y.27, V.32, E.35, M.36, E.131, W.132, M.133, Y.135, H.139, E.140, M.142, H.293, W.294 Ligands: SAH.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.22, A:Y.135 Hydrogen bonds: A:E.35, A:E.131, A:Y.135 Salt bridges: A:E.131, A:E.140 49L.7: 19 residues within 4Å: Chain B: R.19, L.22, Y.23, C.26, Y.27, V.32, E.35, M.36, E.131, W.132, M.133, Y.135, H.139, E.140, M.142, H.293, W.294, N.325 Ligands: SAH.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:R.19, B:L.22, B:Y.23, B:Y.27, B:Y.27, B:Y.135, B:E.140 Hydrogen bonds: B:E.35, B:E.131, B:Y.135 Salt bridges: B:E.131, B:E.140

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: A.91, W.93, Q.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.93 GOL.5: 1 residues within 4Å: Chain A: R.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.97 GOL.8: 11 residues within 4Å: Chain B: L.138, H.139, E.140, S.141, L.243, L.320, P.321, P.326, R.327, R.328, L.329 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.140, B:S.141, B:S.141, B:L.243, B:R.328 Water bridges: B:S.141

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