SMTL ID : 6hs4.1

Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 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: 12 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 Chain F: L.28, F.34 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN-MAN.13: 12 residues within 4Å: Chain B: L.28, F.34 Chain C: L.43, E.129, G.130, A.131, V.153 Chain D: Q.7, P.8, N.62, T.65 Ligands: GOL.24 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.8 NAG-NAG-BMA-MAN-MAN.25: 12 residues within 4Å: Chain D: L.28, F.34 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

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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.227 Hydrogen bonds: A:N.230 Water bridges: A:N.230, A:N.230 NAG.3: 1 residues within 4Å: Chain A: N.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.211 NAG.4: 2 residues within 4Å: Chain A: N.201, E.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.202, A:E.202 NAG.5: 5 residues within 4Å: Chain A: G.237, K.238, R.239, N.241, V.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.238, A:K.238 NAG.11: 3 residues within 4Å: Chain B: N.117, K.121 Chain D: T.115 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:T.115 Hydrogen bonds: B:K.121 NAG.14: 4 residues within 4Å: Chain C: T.190, L.227, N.230, Y.234 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.227 Hydrogen bonds: C:N.230 Water bridges: C:N.230, C:N.230 NAG.15: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.16: 2 residues within 4Å: Chain C: N.201, E.202 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.202, C:E.202 NAG.17: 5 residues within 4Å: Chain C: G.237, K.238, R.239, N.241, V.283 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.238, C:K.238 NAG.23: 3 residues within 4Å: Chain D: N.117, K.121 Chain F: T.115 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:K.121 Hydrophobic interactions: F:T.115 NAG.26: 4 residues within 4Å: Chain E: T.190, L.227, N.230, Y.234 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.227 Hydrogen bonds: E:N.230 Water bridges: E:N.230, E:N.230 NAG.27: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.28: 2 residues within 4Å: Chain E: N.201, E.202 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.202, E:E.202 NAG.29: 5 residues within 4Å: Chain E: G.237, K.238, R.239, N.241, V.283 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.238, E:K.238 NAG.35: 3 residues within 4Å: Chain B: T.115 Chain F: N.117, K.121 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:T.115 Hydrogen bonds: F:K.121

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: W.77, E.79, F.263 Chain B: H.15 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.79, A:E.79 Water bridges: A:E.76, B:N.11, B:H.15 GOL.7: 5 residues within 4Å: Chain A: E.93, C.94, L.95, P.96, D.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.95, A:D.123, A:R.145 Water bridges: A:A.97 GOL.12: 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.18: 4 residues within 4Å: Chain C: W.77, E.79, F.263 Chain D: H.15 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Water bridges: D:N.11, D:H.15, C:E.76 Hydrogen bonds: C:E.79, C:E.79 GOL.19: 5 residues within 4Å: Chain C: E.93, C.94, L.95, P.96, D.123 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.95, C:D.123, C:R.145 Water bridges: C:A.97 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.13 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.62, D:E.63, D:T.65, D:Q.66 GOL.30: 4 residues within 4Å: Chain E: W.77, E.79, F.263 Chain F: H.15 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Water bridges: F:N.11, F:H.15, E:E.76 Hydrogen bonds: E:E.79, E:E.79 GOL.31: 5 residues within 4Å: Chain E: E.93, C.94, L.95, P.96, D.123 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:L.95, E:D.123, E:R.145 Water bridges: E:A.97 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-MAN.25 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.62, F:E.63, F:T.65, F:Q.66

6 x GON: 1-[2-[3-oxidanyl-4-(4-phenyl-1~{H}-pyrazol-5-yl)phenoxy]ethyl]piperidine-4-carboxamide(Non-covalent)

GON.8: 7 residues within 4Å: Chain A: I.11, L.159, P.160, A.162 Chain B: M.47, L.53 Ligands: GON.9 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.53, B:L.53, A:L.159, A:P.160 GON.9: 14 residues within 4Å: Chain A: N.34, R.37, V.39, E.73, A.74 Chain B: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 Chain D: R.86 Ligands: GON.8 16 PLIP interactions: 2 interactions with chain D, 6 interactions with chain A, 8 interactions with chain B Hydrogen bonds: D:R.86, D:R.86, B:Y.16 Hydrophobic interactions: A:R.37, A:V.39, B:L.14, B:Y.16, B:Y.16, B:T.18, B:L.57 Water bridges: A:T.33, A:E.73 Salt bridges: A:E.73, B:D.21 pi-Cation interactions: A:R.37 pi-Stacking: B:Y.16 GON.20: 7 residues within 4Å: Chain C: I.11, L.159, P.160, A.162 Chain D: M.47, L.53 Ligands: GON.21 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.159, C:P.160, D:L.53, D:L.53 GON.21: 14 residues within 4Å: Chain C: N.34, R.37, V.39, E.73, A.74 Chain D: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 Chain F: R.86 Ligands: GON.20 16 PLIP interactions: 6 interactions with chain C, 2 interactions with chain F, 8 interactions with chain D Hydrophobic interactions: C:R.37, C:V.39, D:L.14, D:Y.16, D:Y.16, D:T.18, D:L.57 Water bridges: C:T.33, C:E.73 Salt bridges: C:E.73, D:D.21 pi-Cation interactions: C:R.37 Hydrogen bonds: F:R.86, F:R.86, D:Y.16 pi-Stacking: D:Y.16 GON.32: 7 residues within 4Å: Chain E: I.11, L.159, P.160, A.162 Chain F: M.47, L.53 Ligands: GON.33 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:L.159, E:P.160, F:L.53, F:L.53 GON.33: 14 residues within 4Å: Chain B: R.86 Chain E: N.34, R.37, V.39, E.73, A.74 Chain F: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 Ligands: GON.32 16 PLIP interactions: 6 interactions with chain E, 8 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: E:R.37, E:V.39, F:L.14, F:Y.16, F:Y.16, F:T.18, F:L.57 Water bridges: E:T.33, E:E.73 Salt bridges: E:E.73, F:D.21 pi-Cation interactions: E:R.37 Hydrogen bonds: F:Y.16, B:R.86, B:R.86 pi-Stacking: F:Y.16

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

DMS.10: 6 residues within 4Å: Chain A: V.10, I.11, H.12, 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.22: 6 residues within 4Å: Chain C: V.10, I.11, H.12, 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.34: 6 residues within 4Å: Chain E: V.10, I.11, H.12, D.28, K.29, P.160 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.29 Salt bridges: E:D.28

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,GP1,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,GP1,Envelope glycoprotein

Envelope glycoprotein

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