SMTL ID : 7zvl.1

HUMAN PRMT5:MEP50 Crystal Structure With MTA and Fragment Bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-1-1-mer

Ligands

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

MTA.1: 18 residues within 4Å: Chain A: P.322, L.323, L.327, 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 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.332, A:Y.332, A:G.375, A:K.401, A:N.402, A:D.427, A:M.428, A:R.429 Water bridges: A:L.327 pi-Cation interactions: A:K.401

1 x UNL: UNKNOWN LIGAND

UNL.2: 10 residues within 4Å: Chain A: F.335, K.341, E.443, L.445, G.446, E.452, S.586, W.587 Ligands: MTA.1, CL.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.335, A:F.335, A:E.443 Hydrogen bonds: A:L.445, A:E.452

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: F.48, T.88, V.91, P.128, W.160, Q.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.87, A:Q.271 GOL.5: 9 residues within 4Å: Chain B: N.198, I.200, G.215, C.216, A.218, P.219, G.220, Y.221, F.238 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:I.200, B:C.216, B:A.218, B:G.220, B:Y.221 Water bridges: B:N.198, B:I.200

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: S.586, W.587, F.588 Ligands: UNL.2 Ligand excluded by PLIP

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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