SMTL ID : 8b4f.5 (4 other biounits)

Crystal structure of human cathepsin L forming a thiohemiacetal with N-Boc-2-aminoacetaldehyde

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x OYU: ~{tert}-butyl ~{N}-(2-hydroxyethyl)carbamate(Covalent)(Non-covalent)

OYU.1: 13 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, W.26, G.67, G.68, L.69, A.135, M.161, D.162, H.163, G.164 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.69 Hydrogen bonds: A:Q.19, A:C.25, A:G.68, A:D.162 OYU.9: 14 residues within 4Å: Chain B: Q.19, G.23, S.24, C.25, W.26, G.67, G.68, L.69, M.70, A.135, M.161, D.162, H.163, G.164 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.69, B:A.135 Hydrogen bonds: B:Q.19, B:G.23, B:C.25, B:G.68, B:D.162 OYU.13: 16 residues within 4Å: Chain C: Q.19, C.22, G.23, S.24, C.25, W.26, G.67, G.68, L.69, M.70, A.135, M.161, D.162, H.163, G.164 Ligands: PEG.14 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.69, C:A.135 Hydrogen bonds: C:Q.19, C:G.23, C:C.25, C:G.68, C:D.162 OYU.19: 16 residues within 4Å: Chain D: Q.19, C.22, G.23, S.24, C.25, W.26, G.67, G.68, L.69, M.70, A.135, M.161, D.162, H.163, G.164 Ligands: PEG.24 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.69 Hydrogen bonds: D:Q.19, D:G.23, D:C.25, D:G.68, D:D.162

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

PGE.2: 8 residues within 4Å: Chain A: D.84, S.88, Y.89, P.90, K.99, Y.100, N.101, Y.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.88

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

DMS.3: 2 residues within 4Å: Chain A: S.97, C.98 No protein-ligand interaction detected (PLIP) DMS.22: 11 residues within 4Å: Chain B: R.40, K.124, T.128, V.129 Chain D: P.154, D.155, C.156, S.157, S.158, E.159 Ligands: EDO.23 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Water bridges: B:T.128, B:Y.217 Hydrogen bonds: D:D.155 Salt bridges: D:D.155 DMS.28: 4 residues within 4Å: Chain D: T.14, L.45, I.46, S.47 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.47

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

EDO.4: 7 residues within 4Å: Chain A: D.178, N.179, N.180, K.181, K.203, D.204, R.205 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.179, A:K.181 Water bridges: A:N.180, A:K.203 EDO.6: 7 residues within 4Å: Chain A: C.56, S.57, P.59, Q.60, Y.76, D.79, N.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.60, A:Q.60, A:N.80 EDO.10: 4 residues within 4Å: Chain B: Y.12, F.39, R.40, G.43 No protein-ligand interaction detected (PLIP) EDO.11: 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.16: 7 residues within 4Å: Chain C: C.56, S.57, P.59, Q.60, Y.76, D.79, N.80 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.60 Water bridges: C:Y.76 EDO.17: 6 residues within 4Å: Chain C: K.17, N.18, F.28, E.50, E.86, Y.91 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.18 Water bridges: C:S.47 EDO.23: 12 residues within 4Å: Chain B: R.40, V.113, Y.217 Chain D: F.152, E.153, P.154, D.155, C.156, S.157, H.208, C.209 Ligands: DMS.22 2 PLIP interactions: 2 interactions with chain D Water bridges: D:S.157, D:H.208 EDO.27: 6 residues within 4Å: Chain D: C.56, P.59, Q.60, Y.76, D.79, N.80 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.60, D:N.80 Water bridges: D:C.56

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

PEG.5: 8 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, L.144, W.189 Ligands: NA.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.22 PEG.12: 12 residues within 4Å: Chain A: E.176, S.177, D.178 Chain B: Q.75, Q.78, G.111 Chain D: D.178, N.179, K.181, K.203, D.204, R.205 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:K.181, B:Q.75, B:Q.78 Water bridges: D:D.178, A:S.177 PEG.14: 10 residues within 4Å: Chain C: Q.19, G.20, Q.21, C.22, G.23, S.24, W.189 Chain D: E.141, F.145 Ligands: OYU.13 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.19, C:C.22, D:E.141, D:E.141 Water bridges: C:W.189 PEG.15: 5 residues within 4Å: Chain C: F.39, R.40, K.41, T.42, G.43 No protein-ligand interaction detected (PLIP) PEG.20: 12 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: NA.18, PEG.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.19, D:C.22, D:C.22 PEG.21: 7 residues within 4Å: Chain D: D.84, S.88, Y.89, P.90, K.99, N.101, Y.104 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.92 PEG.24: 8 residues within 4Å: Chain D: A.138, G.139, L.144, D.162, H.163, W.189 Ligands: OYU.19, PEG.20 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.162 PEG.25: 6 residues within 4Å: Chain D: K.17, N.18, F.28, E.50, E.86, Y.91 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.18 PEG.26: 5 residues within 4Å: Chain D: F.39, R.40, K.41, T.42, G.43 No protein-ligand interaction detected (PLIP)

3 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain A: Q.60, Q.75, D.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.79 NA.8: 2 residues within 4Å: Chain A: Q.21 Ligands: PEG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.21, A:Q.21 NA.18: 6 residues within 4Å: Chain C: E.141 Chain D: N.18, Q.19, G.20, W.189 Ligands: PEG.20 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.20, D:G.20

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

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