- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x KH0: ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate(Covalent)
- 11 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.2: 6 residues within 4Å:- Chain A: A.138, G.139, D.162, H.163, W.189
- Ligands: KH0.1
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:D.162
DMS.6: 1 residues within 4Å:- Chain A: C.98
No protein-ligand interaction detected (PLIP)DMS.11: 4 residues within 4Å:- Chain A: S.177, D.178, N.179
- Chain B: Q.75
1 PLIP interactions:1 interactions with chain B- Water bridges: B:Q.75
DMS.17: 3 residues within 4Å:- Chain B: P.59, Q.60, D.79
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.60
- Salt bridges: B:D.79
DMS.18: 5 residues within 4Å:- Chain B: A.138, D.162, H.163, W.189
- Ligands: KH0.12
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:D.162
DMS.20: 5 residues within 4Å:- Chain B: G.20, Q.21, L.144, W.189
- Ligands: KH0.12
2 PLIP interactions:2 interactions with chain B- pi-Cation interactions: B:W.189, B:W.189
DMS.24: 8 residues within 4Å:- Chain B: R.40, T.128, V.129, Y.217
- Chain D: P.154, D.155, C.156, S.157
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:R.40
DMS.26: 4 residues within 4Å:- Chain C: A.138, D.162, W.189
- Ligands: KH0.25
1 PLIP interactions:1 interactions with chain C- Salt bridges: C:D.162
DMS.29: 4 residues within 4Å:- Chain C: E.141
- Chain D: Q.21, L.144, W.189
4 PLIP interactions:2 interactions with chain D, 2 interactions with chain C- pi-Cation interactions: D:W.189, D:W.189
- Hydrogen bonds: C:E.141
- Salt bridges: C:E.141
DMS.33: 5 residues within 4Å:- Chain D: A.138, D.162, H.163, W.189
- Ligands: KH0.31
1 PLIP interactions:1 interactions with chain D- Salt bridges: D:D.162
DMS.34: 3 residues within 4Å:- Chain D: P.59, Q.60, D.79
1 PLIP interactions:1 interactions with chain D- Salt bridges: D:D.79
- 8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.3: 1 residues within 4Å:- Chain A: R.206
No protein-ligand interaction detected (PLIP)PEG.4: 7 residues within 4Å:- Chain A: G.61, E.63, N.66, G.67, G.68, L.69
- Ligands: KH0.1
No protein-ligand interaction detected (PLIP)PEG.5: 5 residues within 4Å:- Chain A: N.18, Q.19, G.20, Y.91, E.92
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.91
PEG.13: 4 residues within 4Å:- Chain B: N.18, G.20, Y.91, A.93
No protein-ligand interaction detected (PLIP)PEG.14: 2 residues within 4Å:- Chain B: E.141, L.144
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:E.141
PEG.21: 8 residues within 4Å:- Chain B: G.61, E.63, N.66, G.67, G.68, L.69, Y.72
- Ligands: KH0.12
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Y.72
PEG.32: 8 residues within 4Å:- Chain D: G.61, E.63, N.66, G.67, G.68, L.69, Y.72
- Ligands: KH0.31
No protein-ligand interaction detected (PLIP)PEG.35: 2 residues within 4Å:- Chain D: P.102, S.105
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:S.105
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.8: 4 residues within 4Å:- Chain A: K.103, Y.104, S.105, V.106
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:S.105
EDO.9: 6 residues within 4Å:- Chain A: E.148, G.149, E.173
- Chain C: E.192
- Chain D: Y.146, E.148
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.148, A:E.148, A:G.149
EDO.10: 6 residues within 4Å:- Chain A: F.145, Y.146, K.147, E.148
- Chain D: E.148, G.149
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:F.145, A:K.147, A:E.148, A:E.148
EDO.15: 3 residues within 4Å:- Chain B: S.88, Y.89, K.99
No protein-ligand interaction detected (PLIP)EDO.16: 3 residues within 4Å:- Chain B: F.39, R.40, G.43
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:R.40
EDO.22: 3 residues within 4Å:- Chain B: G.81, Y.100, P.102
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:G.81
EDO.23: 5 residues within 4Å:- Chain B: W.7, Y.12, R.40, T.128, V.129
5 PLIP interactions:1 interactions with chain D, 4 interactions with chain B- Water bridges: D:E.159, B:R.40
- Hydrogen bonds: B:Y.12, B:R.40, B:R.40
EDO.28: 4 residues within 4Å:- Chain C: S.88, Y.89, K.99, N.101
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:D.84
EDO.36: 4 residues within 4Å:- Chain D: Y.91, E.92, A.93
- Ligands: EDO.37
No protein-ligand interaction detected (PLIP)EDO.37: 5 residues within 4Å:- Chain D: N.18, G.20, Y.91, A.93
- Ligands: EDO.36
No protein-ligand interaction detected (PLIP)- 3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.19: 6 residues within 4Å:- Chain B: S.4, V.5, D.6, W.7, E.9, K.10
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:D.6
- Water bridges: B:V.5, B:V.5, B:D.6
PGE.27: 8 residues within 4Å:- Chain C: G.61, E.63, N.66, G.67, G.68, L.69, Y.72
- Ligands: KH0.25
No protein-ligand interaction detected (PLIP)PGE.30: 4 residues within 4Å:- Chain C: Q.21, W.189
- Chain D: H.140, E.141
3 PLIP interactions:1 interactions with chain C, 2 interactions with chain D- Hydrogen bonds: C:W.189, D:E.141
- Water bridges: D:S.142
- 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
- 2023-08-23
- Peptides
- Cathepsin L: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
SMTL ID : 8prx.1
Crystal structure of human cathepsin L after reaction with the bound ketoamide inhibitor 13b
Cathepsin L
Toggle Identical (ABD)Related Entries With Identical Sequence
2xu1.1 | 2xu1.2 | 2xu1.3 | 2xu1.4 | 3hha.1 | 3hha.2 | 3hha.3 | 3hha.4 | 7qkb.1 | 7qkb.2 | 7qkb.3 | 7qkb.4 | 7qkc.1 | 7qkc.2 | 7qkc.3 | 7qkc.4 | 7qkd.1 | 7qkd.2 | 7qkd.3 | 7qkd.4 | 7z3t.1 | 7z3t.2 | 7z3t.3 | 7z3t.4 | 7z58.1 | 7z58.2 | 7z58.3 | 7z58.4 | 7zs7.1 | 7zs7.2 more...less...7zs7.3 | 7zs7.4 | 7zvf.1 | 7zvf.2 | 7zvf.3 | 7zvf.4 | 7zxa.1 | 7zxa.2 | 7zxa.3 | 7zxa.4 | 8a4u.1 | 8a4u.2 | 8a4u.3 | 8a4u.4 | 8a4v.1 | 8a4v.2 | 8a4v.3 | 8a4v.4 | 8a4w.1 | 8a4w.2 | 8a4w.3 | 8a4w.4 | 8a4x.1 | 8a4x.2 | 8a4x.3 | 8a4x.4 | 8a5b.1 | 8a5b.2 | 8a5b.3 | 8a5b.4 | 8ahv.1 | 8ahv.2 | 8ahv.3 | 8ahv.4 | 8b4f.1 | 8b4f.2 | 8b4f.3 | 8b4f.4 | 8b4f.5 | 8c77.1 | 8c77.2 | 8c77.3 | 8c77.4 | 8ofa.1 | 8ofa.2 | 8ofa.3 | 8ofa.4 | 8oza.1 | 8oza.2 | 8oza.3 | 8oza.4 | 8qkb.1