SMTL ID : 5emj.1

Crystal structure of PRMT5:MEP50 with Compound 8 and sinefungin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

hetero-4-4-mer

Ligands

4 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 20 residues within 4Å: Chain A: L.323, Y.332, K.341, Y.342, G.373, A.374, G.375, P.378, L.379, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 5QJ.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:E.443 Hydrogen bonds: A:Y.332, A:Y.332, A:G.373, A:G.375, A:K.401, A:D.427, A:M.428, A:E.443 Water bridges: A:K.401, A:L.445 Salt bridges: A:K.341 pi-Cation interactions: A:K.401 SFG.7: 20 residues within 4Å: Chain C: L.323, Y.332, K.341, Y.342, G.373, A.374, G.375, P.378, L.379, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 5QJ.8 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:E.443 Hydrogen bonds: C:Y.332, C:Y.332, C:G.373, C:G.375, C:K.401, C:D.427, C:M.428, C:E.443 Water bridges: C:K.401, C:L.445 Salt bridges: C:K.341 pi-Cation interactions: C:K.401 SFG.13: 20 residues within 4Å: Chain E: L.323, Y.332, K.341, Y.342, G.373, A.374, G.375, P.378, L.379, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 5QJ.14 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:E.443 Hydrogen bonds: E:Y.332, E:Y.342, E:G.373, E:G.375, E:K.401, E:D.427, E:M.428, E:E.443 Water bridges: E:K.401, E:L.445 Salt bridges: E:K.341 pi-Cation interactions: E:K.401 SFG.19: 20 residues within 4Å: Chain G: L.323, Y.332, K.341, Y.342, G.373, A.374, G.375, P.378, L.379, E.400, K.401, N.402, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 5QJ.20 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:E.443 Hydrogen bonds: G:Y.332, G:Y.342, G:G.373, G:G.375, G:K.401, G:D.427, G:M.428, G:E.443 Water bridges: G:K.401, G:L.445 Salt bridges: G:K.341 pi-Cation interactions: G:K.401

4 x 5QJ: (2~{S})-1-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-3-[[4-(3-methylbenzimidazol-5-yl)pyridin-2-yl]amino]propan-2-ol(Non-covalent)

5QJ.2: 18 residues within 4Å: Chain A: F.308, Y.312, Q.317, S.318, L.320, L.327, Y.332, F.335, K.341, E.443, L.445, G.446, E.452, V.511, S.586, W.587, F.588 Ligands: SFG.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.320, A:L.327, A:Y.332, A:F.335, A:F.335, A:F.335, A:F.335 Hydrogen bonds: A:L.320 Water bridges: A:L.445, A:E.452, A:E.452, A:E.452, A:S.586 Salt bridges: A:E.443, A:E.452 pi-Stacking: A:F.335 pi-Cation interactions: A:F.335 5QJ.8: 18 residues within 4Å: Chain C: F.308, Y.312, Q.317, S.318, L.320, L.327, Y.332, F.335, K.341, E.443, L.445, G.446, E.452, V.511, S.586, W.587, F.588 Ligands: SFG.7 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.320, C:L.327, C:Y.332, C:F.335, C:F.335, C:F.335, C:F.335 Hydrogen bonds: C:L.320 Water bridges: C:L.445, C:E.452, C:E.452, C:E.452, C:S.586 Salt bridges: C:E.443, C:E.452 pi-Stacking: C:F.335 pi-Cation interactions: C:F.335 5QJ.14: 18 residues within 4Å: Chain E: F.308, Y.312, Q.317, S.318, L.320, L.327, Y.332, F.335, K.341, E.443, L.445, G.446, E.452, V.511, S.586, W.587, F.588 Ligands: SFG.13 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:L.320, E:L.327, E:Y.332, E:F.335, E:F.335, E:F.335, E:F.335 Hydrogen bonds: E:L.320 Water bridges: E:L.445, E:E.452, E:E.452, E:E.452, E:E.452, E:S.586 Salt bridges: E:E.443, E:E.452 pi-Stacking: E:F.335 pi-Cation interactions: E:F.335 5QJ.20: 18 residues within 4Å: Chain G: F.308, Y.312, Q.317, S.318, L.320, L.327, Y.332, F.335, K.341, E.443, L.445, G.446, E.452, V.511, S.586, W.587, F.588 Ligands: SFG.19 18 PLIP interactions: 18 interactions with chain G Hydrophobic interactions: G:L.320, G:L.327, G:Y.332, G:F.335, G:F.335, G:F.335, G:F.335 Hydrogen bonds: G:L.320 Water bridges: G:L.445, G:E.452, G:E.452, G:E.452, G:E.452, G:S.586 Salt bridges: G:E.443, G:E.452 pi-Stacking: G:F.335 pi-Cation interactions: G:F.335

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: N.303, Y.305, H.580, P.582, G.583 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain A: F.48, T.88, W.160, Q.271 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: R.60, E.61, F.62, K.68, Q.74, Q.117 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain B: N.198, I.200, G.215, C.216, P.219, G.220, Y.221, F.238 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain C: N.303, Y.305, H.580, P.582, G.583 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain C: F.48, T.88, W.160, Q.271 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain C: R.60, E.61, F.62, K.68, Q.74, Q.117 Ligand excluded by PLIP GOL.12: 8 residues within 4Å: Chain D: N.198, I.200, G.215, C.216, P.219, G.220, Y.221, F.238 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain E: N.303, Y.305, H.580, P.582, G.583 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain E: F.48, T.88, W.160, Q.271 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain E: R.60, E.61, F.62, K.68, Q.74, Q.117 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain F: N.198, I.200, G.215, C.216, P.219, G.220, Y.221, F.238 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain G: N.303, Y.305, H.580, P.582, G.583 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain G: F.48, T.88, W.160, Q.271 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain G: R.60, E.61, F.62, K.68, Q.74, Q.117 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain H: N.198, I.200, G.215, C.216, P.219, G.220, Y.221, F.238 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duncan, K.W. et al., Structure and Property Guided Design in the Identification of PRMT5 Tool Compound EPZ015666. ACS Med Chem Lett (2016)

Release Date

2016-02-24

Peptides

Protein arginine N-methyltransferase 5: ACEG
Methylosome protein 50: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

Protein arginine N-methyltransferase 5

Methylosome protein 50

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