SMTL ID : 6yyr.1

Structure of Cathepsin S in complex with Compound 20b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: D.87, S.91, Y.92, Q.102, D.104, Y.107 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.87, A:Q.102 Water bridges: A:S.91, A:D.104 EDO.2: 4 residues within 4Å: Chain A: N.165, H.166 Ligands: EDO.5, Q1N.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.166 Water bridges: A:N.165, A:N.165 EDO.3: 2 residues within 4Å: Chain A: E.11, K.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.12 EDO.4: 3 residues within 4Å: Chain A: S.6, D.8, E.11 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.6, A:D.8, A:E.11 EDO.5: 9 residues within 4Å: Chain A: Q.21, G.22, S.23, C.24, G.25, H.166, W.188 Ligands: EDO.2, Q1N.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.21, A:G.22, A:H.166 EDO.9: 5 residues within 4Å: Chain B: S.91, Y.92, Q.102, D.104, Y.107 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.102, B:D.104 EDO.10: 3 residues within 4Å: Chain B: N.165, H.166 Ligands: Q1N.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.166 Water bridges: B:Q.21, B:N.165

2 x FLC: CITRATE ANION(Non-covalent)

FLC.6: 5 residues within 4Å: Chain A: K.46, V.48, S.88, A.90, A.109 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.48 Hydrogen bonds: A:S.88, A:S.88, A:S.88 Water bridges: A:K.46, A:K.46, A:K.46, A:S.49, A:S.49, A:S.91, A:S.91 Salt bridges: A:K.46, A:K.46 FLC.11: 5 residues within 4Å: Chain B: V.18, K.19, Y.20, G.189, H.190 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.20 Hydrogen bonds: B:H.190 Water bridges: B:Y.20, B:Y.20, B:N.191, B:N.191, B:N.191 Salt bridges: B:H.190, B:H.190

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: R.1, P.4, K.12, A.131 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.1 Salt bridges: A:R.1, A:K.12 SO4.12: 2 residues within 4Å: Chain B: S.105, R.108 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.105 Water bridges: B:N.83, B:Y.103, B:R.108, B:R.108 Salt bridges: B:R.108 SO4.13: 1 residues within 4Å: Chain B: R.143 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.143, B:R.143, B:N.165 Salt bridges: B:R.143

2 x Q1N: (2~{R})-~{N}-(2-azanylideneethyl)-2-[2-(3-methyl-1,2-oxazol-5-yl)ethanoylamino]-3-(4-pyridin-2-ylpiperazin-1-yl)sulfonyl-propanamide(Covalent)

Q1N.8: 19 residues within 4Å: Chain A: Q.21, G.25, A.26, C.27, W.28, G.70, G.71, F.72, M.73, E.117, G.139, V.164, N.165, H.166, G.167, F.213 Ligands: EDO.2, EDO.5, Q1N.14 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.72, A:F.72, A:F.213, A:F.213 Hydrogen bonds: A:Q.21, A:C.27, A:G.71, A:G.71, A:N.165, A:H.166 Q1N.14: 19 residues within 4Å: Chain A: F.72 Chain B: Q.21, G.25, A.26, C.27, W.28, G.70, G.71, F.72, M.73, V.138, G.139, V.164, N.165, H.166, G.167, F.213 Ligands: Q1N.8, EDO.10 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.21, B:C.27, B:G.71, B:G.71, B:N.165 pi-Stacking: B:F.213 Hydrophobic interactions: A:F.72, A:F.72

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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