SMTL ID : 9pca.1

HUMAN PRMT5:MEP50 COMPLEX IN COMPLEX WITH LIGAND 18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: (1S,2R,3S,5R)-3-{2-[2-amino-6-(2-hydroxyethyl)quinolin-7-yl]ethyl}-5-(7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclopentane-1,2-diol

01.1: 23 residues within 4Å: Chain A: P.322, L.323, Y.332, F.335, K.341, Y.342, G.373, G.375, P.378, E.400, K.401, N.402, S.426, D.427, M.428, E.443, L.444, L.445, G.446, E.452, C.457, S.586, W.587 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.322, A:L.323, A:F.335, A:F.335, A:E.443 Hydrogen bonds: A:Y.332, A:Y.342, A:Y.342, A:G.375, A:K.401, A:K.401, A:N.402, A:M.428, A:E.452 Water bridges: A:G.377, A:N.402, A:N.402, A:L.445, A:S.447 pi-Cation interactions: A:K.401

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

EDO.2: 5 residues within 4Å: Chain A: F.48, T.88, P.128, W.160, Q.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.88, A:Q.271 Water bridges: A:S.23 EDO.3: 5 residues within 4Å: Chain A: Q.317, V.511, S.586, W.587, F.588 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.317, A:F.588 EDO.4: 6 residues within 4Å: Chain A: E.336, R.376, G.377, P.378, N.381, W.412 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.336, A:N.381, A:N.381 EDO.5: 5 residues within 4Å: Chain A: N.303, Y.305, H.580, S.581, G.583 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.583 EDO.6: 6 residues within 4Å: Chain A: R.60, E.61, F.62, K.68, Q.74, Q.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.61, A:Q.117 Water bridges: A:Q.74 EDO.7: 3 residues within 4Å: Chain A: L.316, S.318, C.495 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.318, A:S.318 Water bridges: A:L.316, A:L.316 EDO.8: 6 residues within 4Å: Chain A: W.194, 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 GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain B: H.272, S.273, H.316 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.273, B:S.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hulpia, F. et al., Discovery of Gut-Restricted PRMT5 Inhibitors to Intercept Colorectal Cancer in Patients with Genetic Loss of Tumor Suppressor Adenomatous Polyposis Coli. J.Med.Chem. (2025)

Release Date

2025-09-10

Peptides

Protein arginine N-methyltransferase 5: A
Methylosome protein WDR77: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein arginine N-methyltransferase 5

Methylosome protein WDR77

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