SMTL ID : 5emm.1

Crystal structure of PRMT5:MEP50 with Compound 15 and sinefungin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 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, E.336, K.341, Y.342, G.373, A.374, G.375, P.378, L.379, E.400, K.401, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 5QL.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.443 Hydrogen bonds: A:Y.332, A:Y.332, A:Y.342, A:G.373, A:G.375, A:K.401, A:D.427, A:M.428, A:R.429, A:E.443 Water bridges: A:E.336, A:E.336, A:K.401 Salt bridges: A:K.341 SFG.5: 20 residues within 4Å: Chain C: L.323, Y.332, E.336, K.341, Y.342, G.373, A.374, G.375, P.378, L.379, E.400, K.401, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 5QL.6 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:E.443 Hydrogen bonds: C:Y.332, C:Y.332, C:Y.342, C:G.373, C:G.375, C:K.401, C:D.427, C:M.428, C:R.429, C:E.443 Water bridges: C:E.336, C:E.336, C:K.401 Salt bridges: C:K.341 SFG.9: 20 residues within 4Å: Chain E: L.323, Y.332, E.336, K.341, Y.342, G.373, A.374, G.375, P.378, L.379, E.400, K.401, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 5QL.10 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:E.443 Hydrogen bonds: E:Y.332, E:G.373, E:G.375, E:K.401, E:D.427, E:M.428, E:R.429, E:E.443 Water bridges: E:E.336, E:K.401 Salt bridges: E:K.341 SFG.13: 20 residues within 4Å: Chain G: L.323, Y.332, E.336, K.341, Y.342, G.373, A.374, G.375, P.378, L.379, E.400, K.401, S.426, D.427, M.428, R.429, E.443, L.444, C.457 Ligands: 5QL.14 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:E.443 Hydrogen bonds: G:Y.332, G:G.373, G:G.375, G:K.401, G:D.427, G:M.428, G:R.429, G:E.443 Water bridges: G:E.336, G:K.401 Salt bridges: G:K.341

4 x 5QL: ~{N}-[(2~{S})-3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-propyl]-3-(oxan-4-ylamino)benzamide

5QL.2: 17 residues within 4Å: Chain A: F.308, Q.317, L.327, V.334, F.335, K.341, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: SFG.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.327, A:F.335, A:F.335, A:F.588, A:F.588, A:F.588 Hydrogen bonds: A:S.447, A:E.452, A:F.588 Water bridges: A:N.451 Salt bridges: A:E.443, A:E.452 pi-Stacking: A:F.335 pi-Cation interactions: A:F.335 5QL.6: 17 residues within 4Å: Chain C: F.308, Q.317, L.327, V.334, F.335, K.341, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: SFG.5 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.327, C:F.335, C:F.335, C:F.588, C:F.588, C:F.588 Hydrogen bonds: C:S.447, C:E.452, C:F.588 Water bridges: C:N.451 Salt bridges: C:E.443, C:E.452 pi-Stacking: C:F.335 pi-Cation interactions: C:F.335 5QL.10: 17 residues within 4Å: Chain E: F.308, Q.317, L.327, V.334, F.335, K.341, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: SFG.9 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:L.327, E:F.335, E:F.335, E:F.588, E:F.588, E:F.588 Hydrogen bonds: E:S.447, E:E.452, E:F.588 Water bridges: E:N.451 Salt bridges: E:E.443, E:E.452 pi-Stacking: E:F.335 pi-Cation interactions: E:F.335 5QL.14: 17 residues within 4Å: Chain G: F.308, Q.317, L.327, V.334, F.335, K.341, E.443, L.445, G.446, S.447, E.452, V.511, F.585, S.586, W.587, F.588 Ligands: SFG.13 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:L.327, G:F.335, G:F.335, G:F.588, G:F.588, G:F.588 Hydrogen bonds: G:S.447, G:E.452, G:F.588 Water bridges: G:N.451 Salt bridges: G:E.443, G:E.452 pi-Stacking: G:F.335 pi-Cation interactions: G:F.335

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: T.88, P.128, W.160, Q.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.271 GOL.4: 4 residues within 4Å: Chain A: N.303, Y.305, E.306, H.580 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.303, A:N.303, A:H.580 GOL.7: 4 residues within 4Å: Chain C: T.88, P.128, W.160, Q.271 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.271 GOL.8: 4 residues within 4Å: Chain C: N.303, Y.305, E.306, H.580 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.303, C:N.303, C:H.580 GOL.11: 4 residues within 4Å: Chain E: T.88, P.128, W.160, Q.271 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.271 GOL.12: 4 residues within 4Å: Chain E: N.303, Y.305, E.306, H.580 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.303, E:N.303, E:E.306, E:H.580 GOL.15: 4 residues within 4Å: Chain G: T.88, P.128, W.160, Q.271 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Q.271 GOL.16: 4 residues within 4Å: Chain G: N.303, Y.305, E.306, H.580 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:N.303, G:N.303, G:E.306, G:H.580

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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