SMTL ID : 7kib.1

PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

hetero-1-1-mer

Ligands

1 x WFM: (2R,3R,3aS,6S,6aR)-6-[(2-amino-3-bromoquinolin-7-yl)oxy]-2-(4-amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl)hexahydro-3aH-cyclopenta[b]furan-3,3a-diol(Non-covalent)

WFM.1: 23 residues within 4Å: Chain A: P.322, L.323, L.327, Y.332, F.335, K.341, G.373, G.375, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, L.445, G.446, E.452, C.457, S.586, W.587 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:P.322, A:L.323, A:L.327, A:Y.332, A:F.335, A:K.401, A:E.443 Hydrogen bonds: A:P.322, A:Y.332, A:G.375, A:E.400, A:K.401, A:D.427, A:M.428, A:E.452 Water bridges: A:N.402, A:L.445, A:S.447 pi-Stacking: A:F.335, A:F.335 pi-Cation interactions: A:K.401 Halogen bonds: A:S.586

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

EDO.2: 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.3: 4 residues within 4Å: Chain A: F.308, Y.312, Q.317 Ligands: PEG.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.317 EDO.4: 3 residues within 4Å: Chain A: L.38, D.85, L.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.85 EDO.5: 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:R.376 Water bridges: A:Q.330 EDO.6: 4 residues within 4Å: Chain A: F.54, Q.74, Q.117, F.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.117 EDO.7: 10 residues within 4Å: Chain A: L.119, G.122, A.123, L.127, A.129, F.130, H.149, S.157, M.158, F.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.127, A:H.149, A:S.157 EDO.8: 5 residues within 4Å: Chain A: K.103, V.104, E.105 Chain B: Y.221, N.242 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.105, B:N.242, B:N.242 Water bridges: A:K.103, A:R.108 EDO.9: 3 residues within 4Å: Chain A: V.550, E.551, G.603 No protein-ligand interaction detected (PLIP) EDO.15: 5 residues within 4Å: Chain B: N.198, I.200, G.215, G.220, Y.221 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.198, B:G.220, B:Y.221 Water bridges: B:N.198, B:I.200 EDO.16: 4 residues within 4Å: Chain A: R.162 Chain B: D.134, K.153, D.154 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.275

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

CL.10: 4 residues within 4Å: Chain A: E.137, D.138, N.139, T.140 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: F.517, H.518, Q.519 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: L.316 Ligand excluded by PLIP

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 7 residues within 4Å: Chain A: D.47, 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:D.47 PEG.14: 9 residues within 4Å: Chain A: Q.317, S.318, L.320, S.447, V.511, S.586, W.587, F.588 Ligands: EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.318, A:S.447, A:F.588

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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