SMTL ID : 6vg5.1

DengueV-2 Capsid ST148 inhibitor Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

28 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 2 residues within 4Å: Chain A: R.66, K.67 Ligand excluded by PLIP NO3.2: 5 residues within 4Å: Chain A: Q.20, T.43, A.44, G.45 Chain B: V.7 Ligand excluded by PLIP NO3.3: 3 residues within 4Å: Chain A: R.63, R.66 Chain B: L.73 Ligand excluded by PLIP NO3.4: 4 residues within 4Å: Chain A: K.26, K.57, N.60, V.61 Ligand excluded by PLIP NO3.5: 3 residues within 4Å: Chain A: V.32, R.36, W.50 Ligand excluded by PLIP NO3.6: 1 residues within 4Å: Chain A: R.13 Ligand excluded by PLIP NO3.9: 1 residues within 4Å: Chain B: R.78 Ligand excluded by PLIP NO3.10: 4 residues within 4Å: Chain B: L.25, R.49, I.53, K.54 Ligand excluded by PLIP NO3.11: 3 residues within 4Å: Chain B: R.63, R.66, K.67 Ligand excluded by PLIP NO3.12: 5 residues within 4Å: Chain A: V.7 Chain B: Q.20, T.43, A.44, G.45 Ligand excluded by PLIP NO3.13: 3 residues within 4Å: Chain B: R.79, R.80, R.81 Ligand excluded by PLIP NO3.14: 2 residues within 4Å: Chain B: R.13, K.26 Ligand excluded by PLIP NO3.15: 5 residues within 4Å: Chain B: S.15, M.18, R.22, G.23, L.27 Ligand excluded by PLIP NO3.16: 3 residues within 4Å: Chain B: V.32, R.36, W.50 Ligand excluded by PLIP NO3.18: 2 residues within 4Å: Chain C: R.66, K.67 Ligand excluded by PLIP NO3.19: 5 residues within 4Å: Chain C: Q.20, T.43, A.44, G.45 Chain D: V.7 Ligand excluded by PLIP NO3.20: 3 residues within 4Å: Chain C: R.63, R.66 Chain D: L.73 Ligand excluded by PLIP NO3.21: 4 residues within 4Å: Chain C: K.26, K.57, N.60, V.61 Ligand excluded by PLIP NO3.22: 3 residues within 4Å: Chain C: V.32, R.36, W.50 Ligand excluded by PLIP NO3.23: 1 residues within 4Å: Chain C: R.13 Ligand excluded by PLIP NO3.26: 1 residues within 4Å: Chain D: R.78 Ligand excluded by PLIP NO3.27: 4 residues within 4Å: Chain D: L.25, R.49, I.53, K.54 Ligand excluded by PLIP NO3.28: 3 residues within 4Å: Chain D: R.63, R.66, K.67 Ligand excluded by PLIP NO3.29: 5 residues within 4Å: Chain C: V.7 Chain D: Q.20, T.43, A.44, G.45 Ligand excluded by PLIP NO3.30: 3 residues within 4Å: Chain D: R.79, R.80, R.81 Ligand excluded by PLIP NO3.31: 2 residues within 4Å: Chain D: R.13, K.26 Ligand excluded by PLIP NO3.32: 5 residues within 4Å: Chain D: S.15, M.18, R.22, G.23, L.27 Ligand excluded by PLIP NO3.33: 3 residues within 4Å: Chain D: V.32, R.36, W.50 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: L.35, R.36, T.39, I.40 Chain B: E.68 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.68 GOL.17: 2 residues within 4Å: Chain B: N.60, V.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.60 Water bridges: B:V.61 GOL.24: 5 residues within 4Å: Chain C: L.35, R.36, T.39, I.40 Chain D: E.68 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.68 GOL.34: 2 residues within 4Å: Chain D: N.60, V.61 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.60 Water bridges: D:V.61

2 x QWY: 3-amino-N-(5-phenyl-1,3,4-thiadiazol-2-yl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]thieno[3,2-e]pyridine-2-carboxamide(Non-covalent)

QWY.8: 14 residues within 4Å: Chain A: T.11, F.14, F.34 Chain B: F.14, S.15, L.16, M.18, L.19, F.34 Chain C: F.14, S.15, L.16, L.19 Ligands: QWY.25 12 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: C:L.19, B:F.14, B:L.19, B:L.19, B:F.34, A:F.14, A:F.34 Water bridges: C:L.16, A:T.11, A:T.11, A:T.11 Hydrogen bonds: B:S.15 QWY.25: 14 residues within 4Å: Chain A: F.14, S.15, L.16, L.19 Chain C: T.11, F.14, F.34 Chain D: F.14, S.15, L.16, M.18, L.19, F.34 Ligands: QWY.8 12 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: C:F.14, C:F.34, D:F.14, D:L.19, D:L.19, D:F.34, A:L.19 Water bridges: C:T.11, C:T.11, A:L.16, A:L.16 Hydrogen bonds: D:S.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, H. et al., A cocrystal structure of dengue capsid protein in complex of inhibitor. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-07-15

Peptides

Capsid premembrane protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Capsid premembrane protein

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