SMTL ID : 7s0u.1

PRMT5/MEP50 crystal structure with MTA and phthalazinone fragment bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-1-1-mer

Ligands

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

CL.1: 1 residues within 4Å: Chain A: S.318 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 1 residues within 4Å: Chain A: Q.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.271, A:Q.271

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: W.194, D.227, R.228, L.230, S.484, H.518, T.554 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.194, A:R.228, A:S.484, A:H.518

1 x 81X: 4-(aminomethyl)phthalazin-1(2H)-one(Non-covalent)

81X.4: 11 residues within 4Å: Chain A: L.320, P.322, F.335, K.341, E.443, L.444, L.445, E.452, S.586, W.587 Ligands: MTA.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.341, A:E.443, A:E.452, A:S.586 pi-Stacking: A:F.335, A:W.587, A:W.587, A:W.587

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

MTA.5: 19 residues within 4Å: Chain A: P.322, L.323, L.327, Y.332, F.335, G.373, G.375, V.399, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 81X.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.332, A:Y.332, A:G.375, A:K.401, A:K.401, A:D.427, A:M.428 pi-Cation interactions: A:K.401

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, C.R. et al., Fragment-Based Discovery of MRTX1719, a Synthetic Lethal Inhibitor of the PRMT5•MTA Complex for the Treatment of MTAP -Deleted Cancers. J.Med.Chem. (2022)

Release Date

2022-01-26

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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