SMTL ID : 7qgw.1

Sulfonated Calpeptin is a promising drug candidate against SARS-CoV-2 infections

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: Q.75, K.78, G.111, F.112 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: R.8, N.197 Chain B: P.15, V.16 Ligands: GOL.15 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain A: K.121, M.124, Q.179, K.182, K.204, D.205 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: F.69, M.70, A.71 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: F.69, M.70, A.71 Ligands: GOL.18 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain B: K.121, M.124, Q.179, K.182, K.204, D.205 Ligand excluded by PLIP

5 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 2 residues within 4Å: Chain A: P.90, V.92 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.90 MPD.8: 6 residues within 4Å: Chain A: A.139, G.140, D.163, H.164, W.190 Ligands: RN2.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.139, A:H.164 Water bridges: A:H.164 MPD.10: 7 residues within 4Å: Chain B: A.139, G.140, D.163, H.164, W.190 Ligands: MPD.17, RN2.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.139 Water bridges: B:D.163 MPD.13: 3 residues within 4Å: Chain B: R.40, K.41, V.221 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.40, B:K.41, B:V.221 Hydrogen bonds: B:R.40 Water bridges: B:V.221 MPD.17: 5 residues within 4Å: Chain B: Q.19, K.20, Q.145, W.190 Ligands: MPD.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.190 Hydrogen bonds: B:K.20

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: F.69, K.160, N.161, L.162 Ligands: RN2.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.160, A:L.162, A:L.162 GOL.7: 7 residues within 4Å: Chain A: T.113, V.115, K.125, A.126, T.129, V.130, Y.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.114, A:T.129, A:Y.218 Water bridges: A:A.116 GOL.12: 3 residues within 4Å: Chain B: P.59, Q.60, G.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.59 GOL.14: 8 residues within 4Å: Chain B: D.84, S.88, Y.89, P.90, K.99, Y.100, R.101, N.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.84, B:R.101, B:R.101, B:N.104 GOL.15: 11 residues within 4Å: Chain A: R.8, N.197, Y.199 Chain B: R.8, V.13, T.14, P.15, V.16, K.187, Y.199 Ligands: CL.2 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.16, B:Y.199, B:Y.199, A:R.8 GOL.18: 7 residues within 4Å: Chain B: A.71, F.112, V.114, A.215, A.216, S.217 Ligands: CL.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.216 Water bridges: B:S.217

2 x RN2: Calpeptin(Covalent)(Non-covalent)

RN2.9: 23 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, W.26, G.61, N.62, Q.63, C.65, N.66, G.67, G.68, F.69, M.70, R.72, A.136, M.137, L.162, D.163, H.164, G.165 Ligands: GOL.5, MPD.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Q.63, A:F.69, A:A.136 Hydrogen bonds: A:Q.19, A:C.25, A:G.68, A:G.68, A:D.163, A:H.164 pi-Stacking: A:F.69 RN2.19: 22 residues within 4Å: Chain B: Q.19, G.23, S.24, C.25, W.26, G.61, N.62, Q.63, C.65, N.66, G.67, G.68, F.69, M.70, R.72, A.136, M.137, L.162, D.163, H.164, G.165 Ligands: MPD.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Q.63, B:F.69, B:F.69, B:A.136 Hydrogen bonds: B:Q.19, B:C.25, B:G.68, B:D.163 Water bridges: B:H.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reinke, P.Y.A. et al., Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections. Commun Biol (2023)

Release Date

2022-12-21

Peptides

Cathepsin L2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cathepsin L2