SMTL ID : 6yyn.1

Structure of Cathepsin S in complex with Compound 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-dimer

Ligands

2 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 2 residues within 4Å: Chain A: Y.156, K.179 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.156 Salt bridges: A:K.179, A:K.179, A:K.204 FLC.2: 3 residues within 4Å: Chain A: V.48, S.88, A.90 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.88, A:S.88 Water bridges: A:K.46, A:S.49, A:S.49

2 x Q1E: ~{N}-methyl-3-[4-([1,2,4]triazolo[4,3-b]pyridazin-6-yl)piperazin-1-yl]sulfonyl-propanamide(Non-covalent)

Q1E.3: 16 residues within 4Å: Chain A: G.25, 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 Chain B: F.72 Ligands: Q1E.10 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.71, A:N.165 Water bridges: A:C.27, A:E.117 pi-Stacking: A:F.213 Hydrophobic interactions: B:F.72 Q1E.10: 17 residues within 4Å: Chain A: F.72, T.74 Chain B: G.25, 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: Q1E.3 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.71, B:N.165, A:T.74 pi-Stacking: B:F.213 Hydrophobic interactions: A:F.72

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

SO4.4: 3 residues within 4Å: Chain B: P.4, D.5, S.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.5, B:S.6 SO4.5: 4 residues within 4Å: Chain B: Y.20, G.22, S.23 Ligands: SO4.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.20, B:S.23 Water bridges: B:S.23, B:S.23, B:S.23 SO4.6: 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 Water bridges: B:N.191, B:N.191 Salt bridges: B:H.190 SO4.7: 3 residues within 4Å: Chain B: R.122, D.124, V.125 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.122 SO4.8: 2 residues within 4Å: Chain B: S.105, R.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.105 Water bridges: B:S.105, B:R.108 Salt bridges: B:R.108 SO4.9: 6 residues within 4Å: Chain B: Y.20, Q.21, G.22, S.187, W.188 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.21, B:G.22

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

Related Entries With Identical Sequence