SMTL ID : 9nnu.1

Crystal Structure of Ebola Envelope glycoprotein GP in complex with compound LD4-189ZbR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 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: 6 residues within 4Å: Chain A: E.125 Chain B: Q.7, P.8, N.62, T.65 Chain F: W.30 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN.7: 6 residues within 4Å: Chain B: W.30 Chain C: E.125 Chain D: Q.7, P.8, N.62, T.65 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.8 NAG-NAG-BMA-MAN.13: 6 residues within 4Å: Chain D: W.30 Chain E: E.125 Chain F: Q.7, P.8, N.62, T.65 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: 3 residues within 4Å: Chain A: T.186, N.226, Y.230 No protein-ligand interaction detected (PLIP) NAG.3: 2 residues within 4Å: Chain A: N.197, E.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.198 NAG.4: 1 residues within 4Å: Chain A: N.207 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: G.233, R.235, N.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.237 NAG.8: 3 residues within 4Å: Chain C: T.186, N.226, Y.230 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain C: N.197, E.198 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.198 NAG.10: 1 residues within 4Å: Chain C: N.207 No protein-ligand interaction detected (PLIP) NAG.11: 3 residues within 4Å: Chain C: G.233, R.235, N.237 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.237 NAG.14: 3 residues within 4Å: Chain E: T.186, N.226, Y.230 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain E: N.197, E.198 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.198 NAG.16: 1 residues within 4Å: Chain E: N.207 No protein-ligand interaction detected (PLIP) NAG.17: 3 residues within 4Å: Chain E: G.233, R.235, N.237 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.237

3 x 01: N-{3-[(1Z)-1-{4-[2-(dimethylamino)ethoxy]phenyl}-1-phenylbut-1-en-2-yl]phenyl}-N'-[(3R)-oxolan-3-yl]sulfuric diamide

01.6: 15 residues within 4Å: Chain A: R.33, V.35, G.36, L.37, E.69, A.70, G.71, L.155 Chain B: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:R.33, A:V.35, A:V.35, A:L.37, A:A.70, A:A.70, A:L.155, B:L.14, B:Y.16, B:Y.16, B:T.18, B:L.57 Salt bridges: A:E.69, B:D.21 Hydrogen bonds: B:Y.16 01.12: 15 residues within 4Å: Chain C: R.33, V.35, G.36, L.37, E.69, A.70, G.71, L.155 Chain D: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 15 PLIP interactions: 7 interactions with chain D, 8 interactions with chain C Hydrophobic interactions: D:L.14, D:Y.16, D:Y.16, D:T.18, D:L.57, C:R.33, C:V.35, C:V.35, C:L.37, C:A.70, C:A.70, C:L.155 Hydrogen bonds: D:Y.16 Salt bridges: D:D.21, C:E.69 01.18: 15 residues within 4Å: Chain E: R.33, V.35, G.36, L.37, E.69, A.70, G.71, L.155 Chain F: L.14, Y.16, T.18, T.19, D.21, M.47, L.57 15 PLIP interactions: 8 interactions with chain E, 7 interactions with chain F Hydrophobic interactions: E:R.33, E:V.35, E:V.35, E:L.37, E:A.70, E:A.70, E:L.155, F:L.14, F:Y.16, F:Y.16, F:T.18, F:L.57 Salt bridges: E:E.69, F:D.21 Hydrogen bonds: F:Y.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dada, L. et al., SuFEx-enabled high-throughput medicinal chemistry for developing potent tamoxifen analogs as Ebola virus entry inhibitors. Front Immunol (2025)

Release Date

2025-07-30

Peptides

Envelope glycoprotein: ACE
GP2: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Envelope glycoprotein

GP2

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