SMTL ID : 7zxa.1 (3 other biounits)

Crystal structure of human cathepsin L with covalently bound aloxistatin (E-64D)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x E6D: ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate(Covalent)

E6D.1: 23 residues within 4Å: Chain A: Q.19, C.22, G.23, S.24, C.25, W.26, G.61, N.62, E.63, N.66, G.67, G.68, L.69, M.70, Y.72, A.135, I.136, M.161, D.162, H.163, G.164, W.189 Ligands: 1PE.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.63, A:Y.72, A:A.135, A:W.189 Hydrogen bonds: A:Q.19, A:C.25, A:G.68, A:G.68, A:D.162 Salt bridges: A:H.163

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 14 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, A.138, G.139, H.140, L.144, D.162, H.163, W.189 Ligands: E6D.1, PEG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.21, A:A.138

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

PG4.3: 9 residues within 4Å: Chain A: D.84, E.87, S.88, Y.89, P.90, K.99, Y.100, N.101, Y.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.88, A:S.88 Water bridges: A:N.101

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

DMS.4: 4 residues within 4Å: Chain A: E.148, G.149, E.173 Ligands: PGE.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.148

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

PEG.5: 8 residues within 4Å: Chain A: Q.21, C.22, G.23, C.65, N.66, A.93, T.94 Ligands: 1PE.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.23, A:A.93 Water bridges: A:E.95

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

PGE.6: 2 residues within 4Å: Chain A: K.103, Y.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.103 PGE.7: 9 residues within 4Å: Chain A: R.8, E.148, G.149, E.173, Y.182, L.184, M.195, K.200 Ligands: DMS.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.8, A:G.149, A:K.200

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

EDO.8: 6 residues within 4Å: Chain A: K.17, N.18, F.28, E.50, E.86, Y.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.18 Water bridges: A:S.47

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

2023-05-31

Peptides

Cathepsin L: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cathepsin L

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