SMTL ID : 7u30.1

PRMT5:MEP50 Complexed with Cyclonucleoside Compound 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: W.194, R.228, L.230, S.484, H.518, T.554 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.194, A:R.228, A:S.484, A:H.518, A:T.554 EDO.2: 4 residues within 4Å: Chain A: S.329, Q.330, E.333, R.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.329, A:Q.330, A:R.376 EDO.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:Q.271 Water bridges: A:T.88 EDO.4: 7 residues within 4Å: Chain A: E.137, D.138, N.139, T.140, W.196, N.199, L.203 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.138, A:N.139, A:N.139, A:T.140, A:W.196, A:F.200 EDO.5: 3 residues within 4Å: Chain A: Y.543, C.544, T.545 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.545, A:T.545 EDO.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain B: N.173, I.175, C.191, A.193, P.194, Y.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.191, B:Y.196 EDO.9: 3 residues within 4Å: Chain B: C.9, E.11, S.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.31

1 x LB3: (9R,10R,11S,12R,13R,14R)-4-amino-9-(3,4-difluorophenyl)-6,7,8,9,10,11,12,13-octahydro-10,13-epoxy[1,3]diazecino[1,2-e]purine-11,12-diol(Non-covalent)

LB3.7: 18 residues within 4Å: Chain A: P.322, L.323, L.327, Y.332, F.335, Y.342, G.373, G.375, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.327 Hydrogen bonds: A:P.322, A:Y.332, A:Y.332, A:G.375, A:K.401, A:D.427, A:M.428

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawamura, S. et al., Design and synthesis of unprecedented 9- and 10-membered cyclonucleosides with PRMT5 inhibitory activity. Bioorg.Med.Chem. (2022)

Release Date

2022-06-01

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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