SMTL ID : 7zuy.1

HUMAN PRMT5:MEP50 Crystal Structure With MTA and Fragment Bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MTA: 5'-DEOXY-5'-METHYLTHIOADENOSINE(Non-covalent)

MTA.1: 17 residues within 4Å: Chain A: P.322, L.323, Y.332, F.335, G.373, G.375, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: UNL.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.332, A:Y.332, A:G.375, A:K.401, A:D.427, A:M.428, A:R.429 Water bridges: A:N.402 pi-Cation interactions: A:K.401

1 x UNL: UNKNOWN LIGAND

UNL.2: 13 residues within 4Å: Chain A: Q.317, S.318, P.319, L.320, F.335, K.341, E.443, L.445, E.452, V.511, S.586, W.587 Ligands: MTA.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.335, A:W.587 Hydrogen bonds: A:L.320, A:K.341, A:E.443, A:L.445, A:S.586 Water bridges: A:E.452 Salt bridges: A:E.452 pi-Stacking: A:W.587

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: F.48, T.88, W.160, Q.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.271, A:Q.271 GOL.4: 9 residues within 4Å: Chain B: N.198, I.200, C.216, A.218, P.219, G.220, Y.221, P.223, F.238 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.198, B:C.216, B:C.216, B:G.220, B:G.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, C.R. et al., Fragment optimization and elaboration strategies - the discovery of two lead series of PRMT5/MTA inhibitors from five fragment hits. Rsc Med Chem (2022)

Release Date

2022-10-19

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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