SMTL ID : 4x60.1

Crystal structure of PRMT5:MEP50 with EPZ015666 and sinefungin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 20 residues within 4Å: Chain A: L.323, Y.332, K.341, Y.342, G.373, A.374, G.375, P.378, L.379, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 3XV.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.332, A:Y.332, A:G.373, A:G.375, A:K.401, A:D.427, A:M.428, A:E.443 Water bridges: A:E.336, A:E.336, A:G.377, A:K.401, A:K.401 Salt bridges: A:K.341 pi-Cation interactions: A:K.401

1 x 3XV: N-[(2S)-3-(3,4-dihydroisoquinolin-2(1H)-yl)-2-hydroxypropyl]-6-(oxetan-3-ylamino)pyrimidine-4-carboxamide(Non-covalent)

3XV.2: 17 residues within 4Å: Chain A: F.308, Y.312, Q.317, L.327, F.335, K.341, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: SFG.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.327, A:F.335, A:F.335, A:F.588 Hydrogen bonds: A:E.452, A:F.585, A:F.588 Water bridges: A:N.451 Salt bridges: A:E.443, A:E.452 pi-Stacking: A:F.335 pi-Cation interactions: A:F.335

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: D.47, F.48, T.88, Q.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.47 GOL.4: 6 residues within 4Å: Chain A: R.60, E.61, F.62, K.68, Q.74, Q.117 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.60, A:K.68, A:Q.117 Water bridges: A:Q.74, A:Q.74, A:Q.74 GOL.5: 6 residues within 4Å: Chain A: N.303, Y.305, H.580, S.581, P.582, G.583 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.303, A:G.583

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan-Penebre, E. et al., A selective inhibitor of PRMT5 with in vivo and in vitro potency in MCL models. Nat.Chem.Biol. (2015)

Release Date

2015-04-22

Peptides

Protein arginine N-methyltransferase 5: A
Methylosome protein 50: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein arginine N-methyltransferase 5

Methylosome protein 50

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