SMTL ID : 7kid.1

PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 72

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 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 EDO.2: 6 residues within 4Å: Chain A: E.137, D.138, N.139, T.140, N.199, L.203 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.138, A:N.139, A:T.140 Water bridges: A:E.137, A:E.137 EDO.3: 4 residues within 4Å: Chain A: S.329, Q.330, E.333, R.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.333, A:R.376 EDO.4: 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

1 x WFV: (1S,2R,3aR,4S,6aR)-4-[(2-amino-3,5-difluoroquinolin-7-yl)methyl]-2-(4-amino-5-fluoro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)hexahydropentalene-1,6a(1H)-diol(Non-covalent)

WFV.5: 21 residues within 4Å: Chain A: P.322, L.323, L.327, Y.332, F.335, K.341, Y.342, G.373, G.375, E.400, K.401, D.427, M.428, E.443, L.444, L.445, G.446, E.452, C.457, S.586, W.587 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:P.322, A:L.327, A:Y.332, A:K.401, A:E.443, A:L.444 Hydrogen bonds: A:Y.332, A:Y.332, A:G.375, A:K.401, A:D.427, A:M.428, A:E.452 Water bridges: A:L.320, A:L.445 pi-Stacking: A:F.335, A:F.335 Halogen bonds: A:Y.342, A:S.586

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quiroz, R.V. et al., The Discovery of Two Novel Classes of 5,5-Bicyclic Nucleoside-Derived PRMT5 Inhibitors for the Treatment of Cancer. J.Med.Chem. (2021)

Release Date

2021-04-21

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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