SMTL ID : 6yyp.1

Structure of Cathepsin S in complex with Compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 3 residues within 4Å: Chain A: L.47, V.48, S.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.49 Water bridges: A:E.17, A:S.49 ACT.2: 6 residues within 4Å: Chain A: L.118, V.125, E.128, A.129, K.133, Y.216 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.125 Salt bridges: A:K.133 ACT.7: 5 residues within 4Å: Chain B: F.72, M.73, T.74, F.213 Ligands: MLA.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.72, B:T.74 Hydrogen bonds: B:M.73, B:T.74, B:T.74 ACT.8: 8 residues within 4Å: Chain B: G.64, N.65, K.66, N.69, G.70, G.71, F.72 Ligands: SIN.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.66 Hydrogen bonds: B:N.69 Salt bridges: B:K.66 ACT.9: 5 residues within 4Å: Chain B: V.18, K.19, Y.20, G.189, H.190 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.190 Water bridges: B:Y.20 Salt bridges: B:H.190 ACT.10: 3 residues within 4Å: Chain B: L.47, V.48, S.49 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.49 Water bridges: B:S.49, B:S.49, B:S.49

1 x Q1H: 1-(furan-2-ylmethyl)-5-(trifluoromethyl)benzimidazol-2-amine(Non-covalent)

Q1H.3: 9 residues within 4Å: Chain A: G.71, F.72, M.73, G.139, V.164, N.165, H.166, G.167, F.213 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.164 Water bridges: A:E.117 pi-Stacking: A:F.72, A:F.72

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.4: 8 residues within 4Å: Chain B: G.71, F.72, M.73, G.139, N.165, H.166, G.167 Ligands: ACT.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.71, B:H.166 Water bridges: B:G.71, B:G.71

2 x MLA: MALONIC ACID(Non-covalent)

MLA.5: 3 residues within 4Å: Chain B: D.124, V.125, E.128 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.125 Hydrogen bonds: B:E.128 MLA.6: 3 residues within 4Å: Chain B: F.72, F.213 Ligands: ACT.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schade, M. et al., Highly Selective Sub-Nanomolar Cathepsin S Inhibitors by Merging Fragment Binders with Nitrile Inhibitors. J.Med.Chem. (2020)

Release Date

2021-05-12

Peptides

Cathepsin S: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Cathepsin S

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