SMTL ID : 6f6s.1

CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH benztropine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-3-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: T.190, L.227, N.230, Y.234 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.227 Hydrogen bonds: A:N.230 NAG.2: 1 residues within 4Å: Chain A: N.201 No protein-ligand interaction detected (PLIP) 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: 3 residues within 4Å: Chain A: G.237, R.239, N.241 No protein-ligand interaction detected (PLIP) NAG.15: 11 residues within 4Å: Chain A: L.43, E.129, G.130, A.131, V.153 Chain B: A.6, Q.7, P.8, N.62, T.65 Ligands: GOL.17 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.65, A:V.153 Hydrogen bonds: B:A.6, B:Q.7, B:N.62, A:E.129 NAG.26: 4 residues within 4Å: Chain C: T.190, L.227, N.230, Y.234 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.227 Hydrogen bonds: C:N.230 NAG.27: 1 residues within 4Å: Chain C: N.201 No protein-ligand interaction detected (PLIP) NAG.28: 1 residues within 4Å: Chain C: N.211 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.211 NAG.29: 3 residues within 4Å: Chain C: G.237, R.239, N.241 No protein-ligand interaction detected (PLIP) NAG.40: 11 residues within 4Å: Chain C: L.43, E.129, G.130, A.131, V.153 Chain D: A.6, Q.7, P.8, N.62, T.65 Ligands: GOL.42 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:T.65, C:V.153 Hydrogen bonds: D:A.6, D:Q.7, D:N.62, C:E.129 NAG.51: 4 residues within 4Å: Chain E: T.190, L.227, N.230, Y.234 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.227 Hydrogen bonds: E:N.230 NAG.52: 1 residues within 4Å: Chain E: N.201 No protein-ligand interaction detected (PLIP) NAG.53: 1 residues within 4Å: Chain E: N.211 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.211 NAG.54: 3 residues within 4Å: Chain E: G.237, R.239, N.241 No protein-ligand interaction detected (PLIP) NAG.65: 11 residues within 4Å: Chain E: L.43, E.129, G.130, A.131, V.153 Chain F: A.6, Q.7, P.8, N.62, T.65 Ligands: GOL.67 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:V.153, F:T.65 Hydrogen bonds: E:E.129, F:A.6, F:Q.7, F:N.62

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: S.63, G.64, P.66, D.123, F.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.64, A:D.123, A:D.123 Water bridges: A:V.65 GOL.6: 9 residues within 4Å: Chain A: N.42, L.43, E.44, T.50, R.58, N.80, Y.82, A.150, E.151 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.44, A:R.58, A:Y.82, A:E.151, A:E.151 GOL.16: 9 residues within 4Å: Chain A: S.38, V.70, N.71, E.73 Chain B: R.79, S.82, I.83, L.84 Chain D: T.80 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.79, B:R.79, B:S.82, B:I.83, B:L.84, A:S.38, A:S.38 Water bridges: A:N.71 GOL.17: 6 residues within 4Å: Chain B: N.62, E.63, T.65, Q.66 Chain F: W.30 Ligands: NAG.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.62, B:E.63, B:T.65, B:Q.66 GOL.18: 5 residues within 4Å: Chain A: R.4, S.5 Chain B: E.1, E.63, A.67 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.5 GOL.30: 5 residues within 4Å: Chain C: S.63, G.64, P.66, D.123, F.124 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.64, C:D.123, C:D.123 Water bridges: C:V.65 GOL.31: 9 residues within 4Å: Chain C: N.42, L.43, E.44, T.50, R.58, N.80, Y.82, A.150, E.151 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.44, C:R.58, C:Y.82, C:E.151, C:E.151 GOL.41: 9 residues within 4Å: Chain C: S.38, V.70, N.71, E.73 Chain D: R.79, S.82, I.83, L.84 Chain F: T.80 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.79, D:R.79, D:S.82, D:I.83, D:L.84, C:S.38, C:S.38 Water bridges: C:N.71 GOL.42: 6 residues within 4Å: Chain B: W.30 Chain D: N.62, E.63, T.65, Q.66 Ligands: NAG.40 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.62, D:E.63, D:T.65, D:Q.66 GOL.43: 5 residues within 4Å: Chain C: R.4, S.5 Chain D: E.1, E.63, A.67 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.5 GOL.55: 5 residues within 4Å: Chain E: S.63, G.64, P.66, D.123, F.124 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.64, E:D.123, E:D.123 Water bridges: E:V.65 GOL.56: 9 residues within 4Å: Chain E: N.42, L.43, E.44, T.50, R.58, N.80, Y.82, A.150, E.151 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.44, E:R.58, E:Y.82, E:E.151, E:E.151 GOL.66: 9 residues within 4Å: Chain B: T.80 Chain E: S.38, V.70, N.71, E.73 Chain F: R.79, S.82, I.83, L.84 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:R.79, F:R.79, F:S.82, F:I.83, F:L.84, E:S.38, E:S.38 Water bridges: E:N.71 GOL.67: 6 residues within 4Å: Chain D: W.30 Chain F: N.62, E.63, T.65, Q.66 Ligands: NAG.65 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.62, F:E.63, F:T.65, F:Q.66 GOL.68: 5 residues within 4Å: Chain E: R.4, S.5 Chain F: E.1, E.63, A.67 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.5

6 x CXQ: benztropine(Non-covalent)

CXQ.7: 6 residues within 4Å: Chain A: R.37, A.74 Chain B: Y.16, Q.20, I.43 Ligands: CXQ.19 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.16, B:Q.20, B:I.43, A:A.74 CXQ.19: 7 residues within 4Å: Chain A: V.39, L.157, L.159 Chain B: Y.16, M.47, L.53 Ligands: CXQ.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.53, A:V.39, A:L.157 pi-Stacking: B:Y.16 CXQ.32: 6 residues within 4Å: Chain C: R.37, A.74 Chain D: Y.16, Q.20, I.43 Ligands: CXQ.44 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.16, D:Q.20, D:I.43, C:A.74 CXQ.44: 7 residues within 4Å: Chain C: V.39, L.157, L.159 Chain D: Y.16, M.47, L.53 Ligands: CXQ.32 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.39, C:L.157, D:L.53 pi-Stacking: D:Y.16 CXQ.57: 6 residues within 4Å: Chain E: R.37, A.74 Chain F: Y.16, Q.20, I.43 Ligands: CXQ.69 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:A.74, F:Y.16, F:Q.20, F:I.43 CXQ.69: 7 residues within 4Å: Chain E: V.39, L.157, L.159 Chain F: Y.16, M.47, L.53 Ligands: CXQ.57 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:V.39, E:L.157, F:L.53 pi-Stacking: F:Y.16

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

DMS.8: 6 residues within 4Å: Chain A: S.5, I.6 Chain B: F.71, R.86, K.87 Ligands: DMS.9 Ligand excluded by PLIP DMS.9: 8 residues within 4Å: Chain A: S.5, D.20, V.21, D.22 Chain B: K.87, D.90 Chain E: S.32 Ligands: DMS.8 Ligand excluded by PLIP DMS.10: 4 residues within 4Å: Chain A: F.105, P.106, V.111, Y.186 Ligand excluded by PLIP DMS.11: 3 residues within 4Å: Chain A: Y.186, Y.187, S.188 Ligand excluded by PLIP DMS.12: 3 residues within 4Å: Chain A: E.93, C.94, D.123 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain A: G.47, V.48, A.49, W.261, A.262 Ligand excluded by PLIP DMS.14: 2 residues within 4Å: Chain A: R.103, G.104 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain A: C.26 Chain B: G.104, C.107, I.109 Chain D: T.99 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain A: V.69 Chain B: E.77, R.79 Ligand excluded by PLIP DMS.22: 3 residues within 4Å: Chain B: N.5, A.6, Q.7 Ligand excluded by PLIP DMS.23: 2 residues within 4Å: Chain B: N.11, N.13 Ligand excluded by PLIP DMS.24: 11 residues within 4Å: Chain B: F.81, S.82, N.85 Chain D: F.81, S.82, N.85 Chain F: F.81, S.82, N.85 Ligands: DMS.49, DMS.74 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain A: L.24 Chain B: Q.94, R.95, D.106 Ligand excluded by PLIP DMS.33: 6 residues within 4Å: Chain C: S.5, I.6 Chain D: F.71, R.86, K.87 Ligands: DMS.34 Ligand excluded by PLIP DMS.34: 8 residues within 4Å: Chain A: S.32 Chain C: S.5, D.20, V.21, D.22 Chain D: K.87, D.90 Ligands: DMS.33 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain C: F.105, P.106, V.111, Y.186 Ligand excluded by PLIP DMS.36: 3 residues within 4Å: Chain C: Y.186, Y.187, S.188 Ligand excluded by PLIP DMS.37: 3 residues within 4Å: Chain C: E.93, C.94, D.123 Ligand excluded by PLIP DMS.38: 5 residues within 4Å: Chain C: G.47, V.48, A.49, W.261, A.262 Ligand excluded by PLIP DMS.39: 2 residues within 4Å: Chain C: R.103, G.104 Ligand excluded by PLIP DMS.45: 5 residues within 4Å: Chain C: C.26 Chain D: G.104, C.107, I.109 Chain F: T.99 Ligand excluded by PLIP DMS.46: 3 residues within 4Å: Chain C: V.69 Chain D: E.77, R.79 Ligand excluded by PLIP DMS.47: 3 residues within 4Å: Chain D: N.5, A.6, Q.7 Ligand excluded by PLIP DMS.48: 2 residues within 4Å: Chain D: N.11, N.13 Ligand excluded by PLIP DMS.49: 11 residues within 4Å: Chain B: F.81, S.82, N.85 Chain D: F.81, S.82, N.85 Chain F: F.81, S.82, N.85 Ligands: DMS.24, DMS.74 Ligand excluded by PLIP DMS.50: 4 residues within 4Å: Chain C: L.24 Chain D: Q.94, R.95, D.106 Ligand excluded by PLIP DMS.58: 6 residues within 4Å: Chain E: S.5, I.6 Chain F: F.71, R.86, K.87 Ligands: DMS.59 Ligand excluded by PLIP DMS.59: 8 residues within 4Å: Chain C: S.32 Chain E: S.5, D.20, V.21, D.22 Chain F: K.87, D.90 Ligands: DMS.58 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain E: F.105, P.106, V.111, Y.186 Ligand excluded by PLIP DMS.61: 3 residues within 4Å: Chain E: Y.186, Y.187, S.188 Ligand excluded by PLIP DMS.62: 3 residues within 4Å: Chain E: E.93, C.94, D.123 Ligand excluded by PLIP DMS.63: 5 residues within 4Å: Chain E: G.47, V.48, A.49, W.261, A.262 Ligand excluded by PLIP DMS.64: 2 residues within 4Å: Chain E: R.103, G.104 Ligand excluded by PLIP DMS.70: 5 residues within 4Å: Chain B: T.99 Chain E: C.26 Chain F: G.104, C.107, I.109 Ligand excluded by PLIP DMS.71: 3 residues within 4Å: Chain E: V.69 Chain F: E.77, R.79 Ligand excluded by PLIP DMS.72: 3 residues within 4Å: Chain F: N.5, A.6, Q.7 Ligand excluded by PLIP DMS.73: 2 residues within 4Å: Chain F: N.11, N.13 Ligand excluded by PLIP DMS.74: 11 residues within 4Å: Chain B: F.81, S.82, N.85 Chain D: F.81, S.82, N.85 Chain F: F.81, S.82, N.85 Ligands: DMS.24, DMS.49 Ligand excluded by PLIP DMS.75: 4 residues within 4Å: Chain E: L.24 Chain F: Q.94, R.95, D.106 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, J. et al., Target Identification and Mode of Action of Four Chemically Divergent Drugs against Ebolavirus Infection. J. Med. Chem. (2018)

Release Date

2018-01-03

Peptides

Envelope glycoprotein,Envelope glycoprotein,GP1: 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,GP1

Envelope glycoprotein

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