SMTL ID : 6hro.1

Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.1: 8 residues within 4Å: Chain A: E.129 Chain B: Q.7, P.8, N.62, T.65 Chain F: L.28, F.34 Ligands: GOL.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.14: 8 residues within 4Å: Chain B: L.28, F.34 Chain C: E.129 Chain D: Q.7, P.8, N.62, T.65 Ligands: GOL.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.27: 8 residues within 4Å: Chain D: L.28, F.34 Chain E: E.129 Chain F: Q.7, P.8, N.62, T.65 Ligands: GOL.37 No protein-ligand interaction detected (PLIP)

15 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.230 Water bridges: A:N.230, A:N.230 NAG.3: 1 residues within 4Å: Chain A: N.211 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: N.201, E.202 No protein-ligand interaction detected (PLIP) NAG.5: 5 residues within 4Å: Chain A: G.237, K.238, R.239, N.241, L.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.238, A:K.238 NAG.10: 2 residues within 4Å: Chain B: N.117 Chain D: T.115 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:T.115 NAG.15: 4 residues within 4Å: Chain C: T.190, L.227, N.230, Y.234 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.230 Water bridges: C:N.230, C:N.230 NAG.16: 1 residues within 4Å: Chain C: N.211 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain C: N.201, E.202 No protein-ligand interaction detected (PLIP) NAG.18: 5 residues within 4Å: Chain C: G.237, K.238, R.239, N.241, L.246 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.238, C:K.238 NAG.23: 2 residues within 4Å: Chain D: N.117 Chain F: T.115 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:T.115 NAG.28: 4 residues within 4Å: Chain E: T.190, L.227, N.230, Y.234 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.230 Water bridges: E:N.230, E:N.230 NAG.29: 1 residues within 4Å: Chain E: N.211 No protein-ligand interaction detected (PLIP) NAG.30: 2 residues within 4Å: Chain E: N.201, E.202 No protein-ligand interaction detected (PLIP) NAG.31: 5 residues within 4Å: Chain E: G.237, K.238, R.239, N.241, L.246 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.238, E:K.238 NAG.36: 2 residues within 4Å: Chain B: T.115 Chain F: N.117 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.115

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.95 Water bridges: A:A.97 GOL.7: 5 residues within 4Å: Chain A: G.64, V.65, P.66, D.123, F.124 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.64, A:D.123, A:D.123 Water bridges: A:V.65, E:R.103 GOL.11: 6 residues within 4Å: Chain B: N.62, E.63, T.65, Q.66 Chain F: W.30 Ligands: NAG-NAG-BMA-MAN-MAN.1 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.62, B:E.63, B:T.65, B:Q.66 GOL.12: 6 residues within 4Å: Chain A: S.5, D.20, V.21 Chain B: K.87, D.90 Chain E: N.34 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:K.87, E:N.34 GOL.19: 5 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.95 Water bridges: C:A.97 GOL.20: 5 residues within 4Å: Chain C: G.64, V.65, P.66, D.123, F.124 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.64, C:D.123, C:D.123 Water bridges: C:V.65, A:R.103 GOL.24: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN-MAN.14 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.62, D:E.63, D:T.65, D:Q.66 GOL.25: 6 residues within 4Å: Chain A: N.34 Chain C: S.5, D.20, V.21 Chain D: K.87, D.90 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.34, D:K.87 GOL.32: 5 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.95 Water bridges: E:A.97 GOL.33: 5 residues within 4Å: Chain E: G.64, V.65, P.66, D.123, F.124 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:G.64, E:D.123, E:D.123 Water bridges: E:V.65, C:R.103 GOL.37: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG-NAG-BMA-MAN-MAN.27 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.62, F:E.63, F:T.65, F:Q.66 GOL.38: 6 residues within 4Å: Chain C: N.34 Chain E: S.5, D.20, V.21 Chain F: K.87, D.90 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:N.34, F:K.87

6 x GKZ: 1-[2-[4-[4-(4-chlorophenyl)-3-methyl-1~{H}-pyrazol-5-yl]-3-oxidanyl-phenoxy]ethyl]piperidin-1-ium-4-carboxamide(Non-covalent)

GKZ.8: 9 residues within 4Å: Chain A: I.11, L.159, P.160, A.162, K.163, K.164 Chain B: M.47, L.53 Ligands: GKZ.13 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.11, A:L.159, A:P.160 Water bridges: A:R.37, A:P.160, A:Q.161 Halogen bonds: B:L.53 GKZ.13: 17 residues within 4Å: Chain A: T.33, N.34, R.37, V.39, G.40, E.73, A.74, G.75 Chain B: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 Chain D: R.86 Ligands: GKZ.8 21 PLIP interactions: 11 interactions with chain B, 8 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: B:L.14, B:Y.16, B:Y.16, B:Y.16, B:T.18, B:M.47, B:L.57, A:V.39, A:A.74, A:A.74 Hydrogen bonds: B:Y.16, B:Y.16, A:T.33, A:R.37, D:R.86, D:R.86 Salt bridges: B:D.21, A:E.73 pi-Stacking: B:Y.16 pi-Cation interactions: A:R.37 Halogen bonds: A:G.40 GKZ.21: 9 residues within 4Å: Chain C: I.11, L.159, P.160, A.162, K.163, K.164 Chain D: M.47, L.53 Ligands: GKZ.26 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.11, C:L.159, C:P.160 Water bridges: C:R.37, C:P.160, C:Q.161 Halogen bonds: D:L.53 GKZ.26: 17 residues within 4Å: Chain C: T.33, N.34, R.37, V.39, G.40, E.73, A.74, G.75 Chain D: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 Chain F: R.86 Ligands: GKZ.21 21 PLIP interactions: 11 interactions with chain D, 8 interactions with chain C, 2 interactions with chain F Hydrophobic interactions: D:L.14, D:Y.16, D:Y.16, D:Y.16, D:T.18, D:M.47, D:L.57, C:V.39, C:A.74, C:A.74 Hydrogen bonds: D:Y.16, D:Y.16, C:T.33, C:R.37, F:R.86, F:R.86 Salt bridges: D:D.21, C:E.73 pi-Stacking: D:Y.16 pi-Cation interactions: C:R.37 Halogen bonds: C:G.40 GKZ.34: 9 residues within 4Å: Chain E: I.11, L.159, P.160, A.162, K.163, K.164 Chain F: M.47, L.53 Ligands: GKZ.39 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:I.11, E:L.159, E:P.160 Water bridges: E:R.37, E:P.160, E:Q.161 Halogen bonds: F:L.53 GKZ.39: 17 residues within 4Å: Chain B: R.86 Chain E: T.33, N.34, R.37, V.39, G.40, E.73, A.74, G.75 Chain F: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 Ligands: GKZ.34 21 PLIP interactions: 11 interactions with chain F, 8 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: F:L.14, F:Y.16, F:Y.16, F:Y.16, F:T.18, F:M.47, F:L.57, E:V.39, E:A.74, E:A.74 Hydrogen bonds: F:Y.16, F:Y.16, E:T.33, E:R.37, B:R.86, B:R.86 Salt bridges: F:D.21, E:E.73 pi-Stacking: F:Y.16 pi-Cation interactions: E:R.37 Halogen bonds: E:G.40

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

DMS.9: 2 residues within 4Å: Chain A: Y.186, S.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.188 DMS.22: 2 residues within 4Å: Chain C: Y.186, S.188 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.188 DMS.35: 2 residues within 4Å: Chain E: Y.186, S.188 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaikh, F. et al., Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library. J.Med.Chem. (2019)

Release Date

2019-02-27

Peptides

Envelope glycoprotein,Envelope glycoprotein,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,Envelope glycoprotein

Envelope glycoprotein

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