SMTL ID : 6yyo.1

Structure of Cathepsin S in complex with Compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: Q.21, G.25, C.27, H.166, W.188 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.21, A:C.27 Salt bridges: A:H.166 SO4.18: 2 residues within 4Å: Chain B: S.105, R.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.105 Water bridges: B:R.108 Salt bridges: B:R.108 SO4.20: 3 residues within 4Å: Chain B: Y.20, G.189, H.190 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.190, B:N.191 Water bridges: B:H.190 Salt bridges: B:H.190 SO4.21: 2 residues within 4Å: Chain B: K.43, H.221 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.43, B:H.221

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

EDO.2: 2 residues within 4Å: Chain A: Y.156, K.204 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: T.16, E.17, L.47, S.49 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: A.142, R.143, F.148, N.165, H.166, W.188 Ligands: SO4.1 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: S.105, R.108 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: D.87, S.91, Y.92, Q.102, D.104, Y.107 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: K.127, E.180, R.202, N.203 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: Y.115, T.116, E.117 Chain B: E.117, L.118, P.119 Ligands: EDO.31 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: K.19, Y.20, Y.94 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: S.6, V.7, D.8, Y.173, Y.181, L.183 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: K.41, K.46, L.47 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: Y.20, G.189, H.190 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: L.176, R.199 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: E.11, K.12 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: K.62 Chain B: G.205 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: Y.20, G.22, S.23, A.96 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: Q.39, L.42, K.43, E.218, I.219 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: D.87, S.91, Y.92, Q.102, D.104, Y.107 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: D.175, N.177, G.178 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: L.40, K.43, T.44, A.110, T.111, I.219 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: D.124, V.125, E.128 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: S.49, D.89, A.90 Ligands: FLC.19 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: Y.63, Y.79, N.83 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: K.127, E.180, R.202, N.203 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain A: E.117, L.118 Chain B: Y.115, T.116, E.117 Ligands: EDO.9 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: K.19, Y.20, F.30, Y.94 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: S.152, G.153, L.176, E.194, R.199 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain B: R.10, V.15, T.16, E.17, V.18, Y.197 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain B: V.7, D.8, W.9, K.12 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain B: Y.156, K.179, K.204 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: V.154, Y.155, Y.156 Ligands: EDO.39 Ligand excluded by PLIP EDO.38: 2 residues within 4Å: Chain A: G.205 Chain B: K.62 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain B: G.153, V.154, K.179 Ligands: EDO.37 Ligand excluded by PLIP

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

DMS.6: 4 residues within 4Å: Chain A: Y.63, Y.79, D.82, N.83 No protein-ligand interaction detected (PLIP)

2 x Q1K: 6-(4-methylsulfonylpiperazin-1-yl)-[1,2,4]triazolo[4,3-b]pyridazine(Non-covalent)

Q1K.17: 13 residues within 4Å: Chain A: G.71, F.72, M.73, E.117, G.139, V.164, N.165, H.166, G.167, F.213 Chain B: F.72, T.74 Ligands: Q1K.40 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B pi-Stacking: A:F.213, A:F.213 Hydrophobic interactions: B:F.72 Q1K.40: 13 residues within 4Å: Chain A: F.72, E.117 Chain B: G.71, F.72, M.73, E.117, G.139, V.164, N.165, H.166, G.167, F.213 Ligands: Q1K.17 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A pi-Stacking: B:F.213 Hydrophobic interactions: A:F.72 Hydrogen bonds: A:T.74

1 x FLC: CITRATE ANION(Non-covalent)

FLC.19: 4 residues within 4Å: Chain B: T.16, E.17, S.49 Ligands: EDO.28 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.17, B:S.49 Water bridges: B:S.49, B:S.49 Salt bridges: B:K.19

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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