SMTL ID : 6nt2.1 (1 other biounit)

type 1 PRMT in complex with the inhibitor GSK3368715

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 20 residues within 4Å: Chain A: Y.57, H.63, M.66, R.72, G.96, S.97, G.98, I.101, L.102, E.118, C.119, S.120, G.144, K.145, V.146, E.147, E.162, M.173, T.176 Ligands: KZS.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.63, A:G.96, A:C.119, A:V.146, A:E.147 Water bridges: A:H.63, A:R.345, A:R.345 Salt bridges: A:R.72 SAH.10: 20 residues within 4Å: Chain B: Y.57, H.63, M.66, R.72, G.96, S.97, I.101, L.102, E.118, C.119, S.120, G.144, K.145, V.146, E.147, E.162, M.173, T.176, R.345 Ligands: KZS.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.96, B:C.119, B:V.146, B:E.147, B:T.176, B:R.345 Water bridges: B:G.100 Salt bridges: B:R.72

2 x KZS: N~1~-({5-[4,4-bis(ethoxymethyl)cyclohexyl]-1H-pyrazol-4-yl}methyl)-N~1~,N~2~-dimethylethane-1,2-diamine(Non-covalent)

KZS.2: 17 residues within 4Å: Chain A: S.56, Y.57, I.62, E.65, M.66, E.162, W.163, M.164, Y.166, Y.170, E.171, M.173, H.311, W.312 Chain B: S.49, Y.53 Ligands: SAH.1 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.57, A:Y.57, A:Y.166, B:Y.53 Hydrogen bonds: A:M.164 Water bridges: A:Y.166 Salt bridges: A:E.162, A:E.171 KZS.11: 19 residues within 4Å: Chain A: S.49, Y.53 Chain B: S.56, Y.57, I.62, E.65, M.66, E.162, W.163, M.164, Y.166, Y.170, E.171, M.173, H.311, W.312, R.345, D.346 Ligands: SAH.10 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.57, B:I.62, B:Y.166, B:R.345, A:Y.53 Hydrogen bonds: B:Y.57, B:M.164, B:Y.166, B:Y.170 Salt bridges: B:E.162, B:E.171

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: W.215, N.218, V.219, Y.220 Chain B: K.68, E.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.218, A:Y.220 GOL.4: 7 residues within 4Å: Chain A: F.169, S.172, N.175, L.265, M.337, P.339, L.347 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.265 Water bridges: A:M.173 GOL.5: 4 residues within 4Å: Chain A: Y.166, V.237, K.313 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.166, A:K.313 Water bridges: A:E.65, A:E.65, A:E.65, A:Y.166 GOL.6: 7 residues within 4Å: Chain A: D.205, Y.208, D.238, V.239, V.240, Q.244 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.238, A:Q.244 GOL.7: 6 residues within 4Å: Chain A: E.204, D.205, R.206, Q.207, Y.208 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.204, A:D.205, A:R.206, A:Q.207, A:Y.208 GOL.8: 6 residues within 4Å: Chain A: Y.170, P.235, V.237, M.370, R.371 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.235, A:V.237 Water bridges: A:Y.170, A:R.371, A:R.371, A:R.371 GOL.9: 7 residues within 4Å: Chain A: N.289, I.290, E.291, R.298, G.300, F.301, S.302 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.289, A:I.290, A:E.291, A:G.300 GOL.12: 7 residues within 4Å: Chain A: L.67, K.68, E.70 Chain B: W.215, N.218, V.219, Y.220 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.67, B:Y.220 Water bridges: A:E.70 GOL.13: 6 residues within 4Å: Chain B: F.169, S.172, N.175, L.265, P.339, L.347 3 PLIP interactions: 3 interactions with chain B Water bridges: B:F.169, B:L.174, B:N.175 GOL.14: 4 residues within 4Å: Chain B: Y.166, V.237, K.313 Ligands: GOL.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.313 Water bridges: B:E.65, B:Y.166 GOL.15: 6 residues within 4Å: Chain B: D.205, Y.208, V.239, V.240, D.241, Q.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.241, B:Q.244 GOL.16: 4 residues within 4Å: Chain B: E.204, R.206, Q.207, Q.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.206, B:Q.207 Water bridges: B:Y.208 GOL.17: 6 residues within 4Å: Chain B: Y.166, Y.170, P.235, V.237, R.371 Ligands: GOL.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.170, B:P.235, B:R.371 Water bridges: B:V.237, B:V.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedoriw, A. et al., Anti-tumor Activity of the Type I PRMT Inhibitor, GSK3368715, Synergizes with PRMT5 Inhibition through MTAP Loss. Cancer Cell (2019)

Release Date

2019-07-10

Peptides

Protein arginine N-methyltransferase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Protein arginine N-methyltransferase 1

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