SMTL ID : 6g95.1

Crystal structure of Ebolavirus glycoprotein in complex with thioridazine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 10 residues within 4Å: Chain A: L.43, E.129, G.130, A.131, V.153 Chain B: Q.7, P.8, N.62, T.65 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN.14: 10 residues within 4Å: Chain C: L.43, E.129, G.130, A.131, V.153 Chain D: Q.7, P.8, N.62, T.65 Ligands: GOL.23 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.8 NAG-NAG-BMA-MAN.27: 10 residues within 4Å: Chain E: L.43, E.129, G.130, A.131, V.153 Chain F: Q.7, P.8, N.62, T.65 Ligands: GOL.36 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:P.8

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: T.190, L.227, N.230, Y.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.230 NAG.3: 2 residues within 4Å: Chain A: N.201, E.202 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain A: N.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.211 NAG.5: 4 residues within 4Å: Chain A: G.237, K.238, N.241, V.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.238 NAG.15: 4 residues within 4Å: Chain C: T.190, L.227, N.230, Y.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.230 NAG.16: 2 residues within 4Å: Chain C: N.201, E.202 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.18: 4 residues within 4Å: Chain C: G.237, K.238, N.241, V.283 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.238 NAG.28: 4 residues within 4Å: Chain E: T.190, L.227, N.230, Y.234 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.230 NAG.29: 2 residues within 4Å: Chain E: N.201, E.202 No protein-ligand interaction detected (PLIP) NAG.30: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.31: 4 residues within 4Å: Chain E: G.237, K.238, N.241, V.283 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.238

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123, R.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.145 Water bridges: A:A.97 GOL.8: 5 residues within 4Å: Chain A: W.77, A.78, E.79 Chain B: H.15 Ligands: DMS.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.79, A:E.79, B:H.15 GOL.10: 6 residues within 4Å: Chain B: N.62, E.63, T.65, Q.66 Chain F: W.30 Ligands: NAG-NAG-BMA-MAN.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.62, B:T.65, B:Q.66 GOL.11: 7 residues within 4Å: Chain A: A.15, L.16 Chain B: I.3, D.51, G.52, L.53, G.56 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.3, B:D.51, A:L.16 GOL.19: 6 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123, R.145 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.145 Water bridges: C:A.97 GOL.21: 5 residues within 4Å: Chain C: W.77, A.78, E.79 Chain D: H.15 Ligands: DMS.25 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.79, C:E.79, D:H.15 GOL.23: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.62, D:T.65, D:Q.66 GOL.24: 7 residues within 4Å: Chain C: A.15, L.16 Chain D: I.3, D.51, G.52, L.53, G.56 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:I.3, D:D.51, C:L.16 GOL.32: 6 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123, R.145 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.145 Water bridges: E:A.97 GOL.34: 5 residues within 4Å: Chain E: W.77, A.78, E.79 Chain F: H.15 Ligands: DMS.38 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:H.15, E:E.79, E:E.79 GOL.36: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN.27 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.62, F:T.65, F:Q.66 GOL.37: 7 residues within 4Å: Chain E: A.15, L.16 Chain F: I.3, D.51, G.52, L.53, G.56 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:I.3, F:D.51, E:L.16

9 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 3 residues within 4Å: Chain A: Y.186, Y.187, S.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.188 DMS.9: 5 residues within 4Å: Chain A: V.10, I.11, D.28, K.29, P.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.29 Salt bridges: A:D.28 DMS.12: 5 residues within 4Å: Chain A: W.264 Chain B: N.11, H.15, L.46 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.11 Water bridges: B:H.15 DMS.20: 3 residues within 4Å: Chain C: Y.186, Y.187, S.188 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.188 DMS.22: 5 residues within 4Å: Chain C: V.10, I.11, D.28, K.29, P.160 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.29 Salt bridges: C:D.28 DMS.25: 5 residues within 4Å: Chain C: W.264 Chain D: N.11, H.15, L.46 Ligands: GOL.21 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.11 Water bridges: D:H.15 DMS.33: 3 residues within 4Å: Chain E: Y.186, Y.187, S.188 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.188 DMS.35: 5 residues within 4Å: Chain E: V.10, I.11, D.28, K.29, P.160 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.29 Salt bridges: E:D.28 DMS.38: 5 residues within 4Å: Chain E: W.264 Chain F: N.11, H.15, L.46 Ligands: GOL.34 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.11 Water bridges: F:H.15

3 x RTZ: 10-{2-[(2R)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine(Non-covalent)

RTZ.13: 12 residues within 4Å: Chain A: G.9, V.10, I.11, L.16, L.157, I.158, L.159 Chain B: L.14, M.47, H.48, L.53, I.54 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.14, B:M.47, B:I.54, A:I.11, A:L.16, A:L.157 RTZ.26: 12 residues within 4Å: Chain C: G.9, V.10, I.11, L.16, L.157, I.158, L.159 Chain D: L.14, M.47, H.48, L.53, I.54 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.11, C:L.16, C:L.157, D:L.14, D:M.47, D:I.54 RTZ.39: 12 residues within 4Å: Chain E: G.9, V.10, I.11, L.16, L.157, I.158, L.159 Chain F: L.14, M.47, H.48, L.53, I.54 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:L.14, F:M.47, F:I.54, E:I.11, E:L.16, E:L.157

Links

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Citation

Zhao, Y. et al., Structures of Ebola Virus Glycoprotein Complexes with Tricyclic Antidepressant and Antipsychotic Drugs. J. Med. Chem. (2018)

Release Date

2018-05-23

Peptides

Envelope glycoprotein: ACE
Envelope glycoprotein: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Envelope glycoprotein

Envelope glycoprotein

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