SMTL ID : 3q3y.1 (2 other biounits)

Complex structure of HEVB EV93 main protease 3C with Compound 1 (AG7404)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

monomer

Ligands

1 x XNV: ethyl (4R)-4-({(2S)-2-[3-{[(5-methyl-1,2-oxazol-3-yl)carbonyl]amino}-2-oxopyridin-1(2H)-yl]pent-4-ynoyl}amino)-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate(Covalent)

XNV.1: 18 residues within 4Å: Chain A: H.42, E.73, L.127, N.128, L.129, G.130, T.144, A.146, G.147, C.149, H.163, V.164, G.165, G.166, N.167, Q.170, F.172 Ligands: EDO.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:H.42, A:L.127, A:F.172 Hydrogen bonds: A:G.130, A:T.144, A:G.147, A:V.164, A:G.166, A:G.166 Water bridges: A:G.131, A:C.149, A:N.167, A:N.167, A:N.167, A:N.167

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: Y.33, W.36, K.62, L.76, Y.180, F.181, N.182 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.33, A:K.62, A:Y.180, A:N.182 EDO.3: 4 residues within 4Å: Chain A: K.21, T.22, T.48, L.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.21, A:L.50 Water bridges: A:E.23 EDO.4: 2 residues within 4Å: Chain A: G.130 Ligands: XNV.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.130 EDO.5: 3 residues within 4Å: Chain A: F.8, F.91, G.157 No protein-ligand interaction detected (PLIP)

2 x PI: HYDROGENPHOSPHATE ION(Non-covalent)

PI.6: 4 residues within 4Å: Chain A: D.66, K.67, R.136, H.179 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.67 Water bridges: A:R.136, A:R.136, A:R.136 Salt bridges: A:R.136, A:H.179 PI.7: 4 residues within 4Å: Chain A: M.51, Q.54, V.56, R.81 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.81, A:R.81, A:R.81 Salt bridges: A:R.81

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.8: 3 residues within 4Å: Chain A: E.23, Y.24, K.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.23, A:E.23 NH4.9: 1 residues within 4Å: Chain A: N.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Costenaro, L. et al., Structural Basis for Antiviral Inhibition of the Main Protease, 3C, from Human Enterovirus 93. J.Virol. (2011)

Release Date

2011-09-07

Peptides

HEVB EV93 3C protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HEVB EV93 3C protease

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