SMTL ID : 8prx.1

Crystal structure of human cathepsin L after reaction with the bound ketoamide inhibitor 13b

Coordinates

PDB Format Compare

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)

KH0.1: 17 residues within 4Å: Chain A: Q.19, C.22, G.23, S.24, C.25, W.26, C.65, N.66, G.67, G.68, L.69, A.135, M.161, D.162, H.163 Ligands: DMS.2, PEG.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.69, A:A.135 Hydrogen bonds: A:Q.19, A:C.25, A:G.68, A:D.162, A:H.163 KH0.12: 19 residues within 4Å: Chain A: A.1, R.3 Chain B: Q.19, C.22, G.23, S.24, C.25, W.26, C.65, N.66, G.67, G.68, L.69, A.135, D.162, H.163 Ligands: DMS.18, DMS.20, PEG.21 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.69, B:A.135 Hydrogen bonds: B:Q.19, B:C.25, B:G.68, B:D.162, B:H.163 KH0.25: 19 residues within 4Å: Chain C: Q.19, Q.21, C.22, G.23, S.24, C.25, W.26, C.65, N.66, G.67, G.68, L.69, M.70, A.135, D.162, H.163, W.189 Ligands: DMS.26, PGE.27 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.69, C:A.135 Hydrogen bonds: C:Q.19, C:C.25, C:G.68, C:D.162, C:H.163 KH0.31: 18 residues within 4Å: Chain D: Q.19, Q.21, C.22, G.23, S.24, C.25, W.26, C.65, N.66, G.67, G.68, L.69, A.135, D.162, H.163, W.189 Ligands: PEG.32, DMS.33 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.69, D:A.135 Hydrogen bonds: D:Q.19, D:C.25, D:G.68, D:D.162, D:H.163

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 C, 2 interactions with chain D Hydrogen bonds: C:E.141 Salt bridges: C:E.141 pi-Cation interactions: D:W.189, D:W.189 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)

PG4.7: 4 residues within 4Å: Chain A: S.88, Y.89, K.99, Y.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.101

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: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.12, B:R.40, B:R.40 Water bridges: B:R.40, D:E.159 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
A

B
B

C
C

D
D

Cathepsin L

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