SMTL ID : 8e7c.1

Crystal Structure of Porcine Deltacoronavirus (HKU-15) Mpro with Pfizer Intravenous Inhibitor PF-00835231

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x V2M: N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide(Covalent)

V2M.1: 17 residues within 4Å: Chain A: L.27, H.41, K.45, F.139, L.140, N.141, G.142, A.143, C.144, H.162, H.163, I.164, E.165, H.171, D.186, E.188, V.189 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:H.41, A:K.45, A:I.164, A:D.186, A:E.188, A:E.188 Hydrogen bonds: A:F.139, A:N.141, A:G.142, A:C.144, A:H.163, A:E.165, A:E.165, A:E.188, A:E.188 Water bridges: A:A.26 V2M.12: 17 residues within 4Å: Chain B: A.26, L.27, H.41, K.45, F.139, L.140, N.141, G.142, A.143, C.144, H.162, H.163, I.164, E.165, H.171, D.186, E.188 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.45, B:I.164, B:D.186, B:E.188 Hydrogen bonds: B:F.139, B:N.141, B:G.142, B:A.143, B:C.144, B:H.163, B:E.165, B:E.165, B:E.188 Water bridges: A:A.1

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Chain A: S.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.56 GOL.3: 5 residues within 4Å: Chain A: C.60, R.61, F.63, N.75, V.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.60, A:N.75, A:V.76 GOL.4: 4 residues within 4Å: Chain A: Y.117, H.123, L.140 Ligands: DMS.19 No protein-ligand interaction detected (PLIP) GOL.5: 4 residues within 4Å: Chain A: K.152, G.153 Chain B: R.122, H.123 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:R.122 Hydrogen bonds: A:G.153 GOL.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.8: 2 residues within 4Å: Chain A: K.4 Chain B: D.292 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.292, B:D.292 GOL.9: 2 residues within 4Å: Chain A: Y.136, F.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.136 Water bridges: A:N.132 GOL.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.11: 6 residues within 4Å: Chain A: V.55, S.56, A.58, C.60, S.78, V.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.56, A:V.79 GOL.13: 6 residues within 4Å: Chain B: K.66, C.67, P.68, G.71, I.72 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.66, B:I.72 GOL.14: 3 residues within 4Å: Chain B: K.66, G.71 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.66, B:K.66 GOL.15: 2 residues within 4Å: Chain B: N.232, S.233 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.233 Water bridges: B:N.232 GOL.16: 4 residues within 4Å: Chain A: H.123 Chain B: H.8, M.297, N.300 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:H.123, B:H.8, B:E.296, B:N.300

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

DMS.6: 2 residues within 4Å: Chain A: K.101, Y.157 No protein-ligand interaction detected (PLIP) DMS.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) DMS.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) DMS.19: 1 residues within 4Å: Ligands: GOL.4 No protein-ligand interaction detected (PLIP) DMS.20: 2 residues within 4Å: Chain B: Y.117, D.118 No protein-ligand interaction detected (PLIP) DMS.21: 2 residues within 4Å: Chain B: V.189, I.190 No protein-ligand interaction detected (PLIP) DMS.22: 1 residues within 4Å: Chain B: K.80 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zvornicanin, S.N. et al., Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses. Viruses (2023)

Release Date

2023-03-29

Peptides

Main Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Main Protease