SMTL ID : 5eml.1

Crystal structure of PRMT5:MEP50 with Compound 10 and SAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-4-4-mer

Ligands

4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 20 residues within 4Å: Chain A: P.322, L.323, Y.332, K.341, Y.342, G.373, 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: 5QK.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.332, A:Y.332, A:G.373, A:G.375, A:K.401, A:D.427, A:M.428 Water bridges: A:E.336, A:N.402 Salt bridges: A:K.341, A:E.443 pi-Cation interactions: A:K.401 SAM.5: 20 residues within 4Å: Chain C: P.322, L.323, Y.332, K.341, Y.342, G.373, 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: 5QK.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:Y.332, C:Y.332, C:G.373, C:G.375, C:K.401, C:D.427, C:M.428 Water bridges: C:E.336, C:N.402 Salt bridges: C:K.341, C:E.443 pi-Cation interactions: C:K.401 SAM.9: 20 residues within 4Å: Chain E: P.322, L.323, Y.332, K.341, Y.342, G.373, 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: 5QK.10 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:Y.332, E:Y.342, E:G.373, E:G.375, E:K.401, E:D.427, E:M.428 Water bridges: E:N.402 Salt bridges: E:K.341, E:E.443 pi-Cation interactions: E:K.401 SAM.13: 20 residues within 4Å: Chain G: P.322, L.323, Y.332, K.341, Y.342, G.373, 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: 5QK.14 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:Y.332, G:Y.342, G:G.373, G:G.375, G:K.401, G:D.427, G:M.428 Water bridges: G:N.402 Salt bridges: G:K.341, G:E.443 pi-Cation interactions: G:K.401

4 x 5QK: ~{N}-[(2~{R})-3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-propyl]-2-quinolin-8-yloxy-ethanamide(Non-covalent)

5QK.2: 16 residues within 4Å: Chain A: F.308, Y.312, Q.317, L.320, L.327, T.331, F.335, K.341, E.443, S.447, E.452, V.511, S.586, W.587, F.588 Ligands: SAM.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.308, A:Y.312, A:L.320, A:L.327, A:F.335, A:F.335, A:F.335, A:F.588 Hydrogen bonds: A:Q.317, A:L.445, A:F.588 Water bridges: A:L.320 Salt bridges: A:E.443, A:E.452 pi-Stacking: A:F.335, A:F.335 pi-Cation interactions: A:F.335 5QK.6: 16 residues within 4Å: Chain C: F.308, Y.312, Q.317, L.320, L.327, T.331, F.335, K.341, E.443, S.447, E.452, V.511, S.586, W.587, F.588 Ligands: SAM.5 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.308, C:Y.312, C:L.320, C:L.327, C:F.335, C:F.335, C:F.335, C:F.588 Hydrogen bonds: C:Q.317, C:L.445, C:F.588 Water bridges: C:L.320 Salt bridges: C:E.443, C:E.452 pi-Stacking: C:F.335, C:F.335 pi-Cation interactions: C:F.335 5QK.10: 16 residues within 4Å: Chain E: F.308, Y.312, Q.317, L.320, L.327, T.331, F.335, K.341, E.443, S.447, E.452, V.511, S.586, W.587, F.588 Ligands: SAM.9 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:F.308, E:Y.312, E:L.320, E:L.327, E:F.335, E:F.335, E:F.335, E:F.588 Hydrogen bonds: E:Q.317, E:L.445, E:F.588 Water bridges: E:E.452 Salt bridges: E:E.443, E:E.452 pi-Stacking: E:F.335, E:F.335 pi-Cation interactions: E:F.335 5QK.14: 16 residues within 4Å: Chain G: F.308, Y.312, Q.317, L.320, L.327, T.331, F.335, K.341, E.443, S.447, E.452, V.511, S.586, W.587, F.588 Ligands: SAM.13 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:F.308, G:Y.312, G:L.320, G:L.327, G:F.335, G:F.335, G:F.335, G:F.588 Hydrogen bonds: G:Q.317, G:L.445, G:F.588 Water bridges: G:E.452 Salt bridges: G:E.443, G:E.452 pi-Stacking: G:F.335, G:F.335 pi-Cation interactions: G:F.335

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: F.48, T.88, W.160, Q.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.271, A:Q.271 GOL.4: 8 residues within 4Å: Chain B: N.198, I.200, C.216, A.218, P.219, G.220, Y.221, P.223 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.198, B:C.216, B:G.220, B:G.220 Water bridges: B:I.200 GOL.7: 4 residues within 4Å: Chain C: F.48, T.88, W.160, Q.271 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.271, C:Q.271 GOL.8: 8 residues within 4Å: Chain D: N.198, I.200, C.216, A.218, P.219, G.220, Y.221, P.223 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.198, D:C.216, D:G.220, D:G.220 Water bridges: D:I.200 GOL.11: 4 residues within 4Å: Chain E: F.48, T.88, W.160, Q.271 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.271, E:Q.271 GOL.12: 8 residues within 4Å: Chain F: N.198, I.200, C.216, A.218, P.219, G.220, Y.221, P.223 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:N.198, F:C.216, F:G.220, F:G.220 Water bridges: F:I.200 GOL.15: 4 residues within 4Å: Chain G: F.48, T.88, W.160, Q.271 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.271, G:Q.271 GOL.16: 8 residues within 4Å: Chain H: N.198, I.200, C.216, A.218, P.219, G.220, Y.221, P.223 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:N.198, H:C.216, H:G.220, H:G.220 Water bridges: H:I.200

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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