SMTL ID : 8qkb.1

Crystal structure of human cathepsin L in complex with the vinyl sulfone inhibitor K777

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x D1R: NALPHA-[(4-METHYLPIPERAZIN-1-YL)CARBONYL]-N-{(1S)-3-PHENYL-1-[2-(PHENYLSULFONYL)ETHYL]PROPYL}-L-PHENYLALANINAMIDE(Non-covalent)(Covalent)

D1R.1: 21 residues within 4Å: Chain A: Q.19, G.23, C.25, W.26, G.61, E.63, C.65, N.66, G.67, G.68, L.69, M.70, A.135, A.138, M.161, D.162, H.163, G.164, W.189, A.214 Ligands: PEG.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.69, A:A.135, A:A.138, A:H.163, A:A.214 Hydrogen bonds: A:G.68, A:G.68, A:D.162 Salt bridges: A:E.63 pi-Stacking: A:H.163, A:W.189 D1R.10: 20 residues within 4Å: Chain B: Q.19, G.23, C.25, W.26, G.61, E.63, C.65, N.66, G.67, G.68, L.69, M.70, A.135, A.138, M.161, D.162, H.163, G.164, W.189 Ligands: PGE.11 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.69, B:A.135, B:A.138, B:H.163 Hydrogen bonds: B:G.68, B:G.68, B:D.162 Salt bridges: B:E.63 pi-Stacking: B:H.163, B:W.189 D1R.19: 19 residues within 4Å: Chain C: Q.19, G.23, C.25, W.26, G.61, E.63, C.65, G.67, G.68, L.69, A.135, A.138, M.161, D.162, H.163, G.164, W.189 Ligands: DMS.23, PEG.24 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.69, C:A.135, C:A.138, C:H.163 Hydrogen bonds: C:G.68, C:G.68, C:D.162 pi-Stacking: C:W.189 D1R.25: 20 residues within 4Å: Chain D: Q.19, G.23, C.25, W.26, G.61, E.63, C.65, N.66, G.67, G.68, L.69, A.135, A.138, M.161, D.162, H.163, G.164, W.189, A.214 Ligands: PGE.30 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.69, D:A.135, D:A.138, D:H.163, D:A.214 Hydrogen bonds: D:G.68, D:G.68, D:D.162 Salt bridges: D:E.63 pi-Stacking: D:H.163, D:W.189

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 6 residues within 4Å: Chain A: E.87, S.88, Y.89, P.90, K.99, Y.104 No protein-ligand interaction detected (PLIP)

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

EDO.3: 1 residues within 4Å: Chain A: K.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.103 EDO.4: 7 residues within 4Å: Chain A: N.18, Q.19, G.20, Y.91, E.92, A.93 Ligands: PEG.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.18 EDO.5: 4 residues within 4Å: Chain A: Q.37, R.40, K.41, V.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.37, A:V.220 Water bridges: A:V.220 EDO.7: 3 residues within 4Å: Chain A: D.79, N.80, G.81 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain B: N.18, G.20, Y.91, E.92, A.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.91 EDO.13: 4 residues within 4Å: Chain B: S.88, Y.89, P.90, K.99 No protein-ligand interaction detected (PLIP) EDO.15: 5 residues within 4Å: Chain B: S.4, V.5, D.6, W.7, K.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.6 EDO.16: 5 residues within 4Å: Chain B: Q.21, C.22, G.23, C.65 Ligands: PGE.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.23, B:C.65 Water bridges: B:T.94 EDO.17: 6 residues within 4Å: Chain B: Q.118, K.120 Chain C: Q.19, G.20, Q.21, A.93 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.120, B:K.120, C:Q.21 EDO.22: 3 residues within 4Å: Chain C: S.88, Y.89, K.99 No protein-ligand interaction detected (PLIP) EDO.29: 1 residues within 4Å: Chain D: C.98 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:C.98 Water bridges: D:S.97, D:S.97, D:C.98 EDO.31: 5 residues within 4Å: Chain D: L.69, D.71, Y.72, F.112, D.114 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.71, D:D.114

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 9 residues within 4Å: Chain A: K.17, N.18, Q.19, F.28, E.50, E.86, Y.91 Chain C: E.9 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.18 Water bridges: A:S.47, A:Y.91 PEG.8: 7 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, L.144, W.189 Ligands: D1R.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.21 PEG.20: 5 residues within 4Å: Chain C: F.39, R.40, K.41, T.42, G.43 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.42 PEG.24: 10 residues within 4Å: Chain C: Q.19, G.20, Q.21, C.22, L.144, W.189 Chain D: E.141, L.144, F.145 Ligands: D1R.19 No protein-ligand interaction detected (PLIP) PEG.26: 7 residues within 4Å: Chain D: D.84, S.88, Y.89, P.90, K.99, N.101, Y.104 No protein-ligand interaction detected (PLIP)

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

DMS.9: 3 residues within 4Å: Chain A: P.59, Q.60, D.79 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.79 DMS.14: 6 residues within 4Å: Chain B: W.7, Y.12, R.40, T.128, V.129, G.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.40 DMS.18: 7 residues within 4Å: Chain B: R.40, T.128, V.129, Y.217 Chain D: P.154, D.155, C.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.40, B:R.40 DMS.21: 3 residues within 4Å: Chain C: P.59, Q.60, D.79 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:D.79 DMS.23: 5 residues within 4Å: Chain C: L.69, D.71, D.114, A.214 Ligands: D1R.19 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.71 Salt bridges: C:D.71 DMS.27: 3 residues within 4Å: Chain D: P.59, Q.60, D.79 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.60 Salt bridges: D:D.79

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 9 residues within 4Å: Chain B: Q.19, G.20, Q.21, C.22, G.23, L.144, W.189 Ligands: D1R.10, EDO.16 No protein-ligand interaction detected (PLIP) PGE.28: 6 residues within 4Å: Chain D: N.18, Q.19, G.20, Y.91, E.92, A.93 No protein-ligand interaction detected (PLIP) PGE.30: 11 residues within 4Å: Chain C: E.141, L.144, F.145 Chain D: Q.19, G.20, Q.21, C.22, G.23, L.144, W.189 Ligands: D1R.25 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Falke, S. et al., Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors. J.Med.Chem. (2024)

Release Date

2023-09-27

Peptides

Cathepsin L: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cathepsin L

Related Entries With Identical Sequence