SMTL ID : 9g6a.1

Peptide-Small Molecule Hybrids as Novel Selective Irreversible Cathepsin-K Inhibitors in Primary Osteoclasts and Human Lung Cancer Tissue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

2 x 01: (2~{S})-4-methyl-~{N}-(2-oxidanylidenepropyl)-2-[[(1~{S})-2,2,2-tris(fluoranyl)-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide

01.1: 21 residues within 4Å: Chain A: Q.20, G.24, S.25, C.26, W.27, S.59, E.60, N.61, D.62, G.65, G.66, G.67, Y.68, M.69, A.135, L.161, N.162, H.163 Chain B: Y.68, L.210 Ligands: PGE.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.62, A:L.161 Hydrogen bonds: A:Q.20, A:C.26, A:G.67, A:N.162 pi-Stacking: A:Y.68 Halogen bonds: A:Y.68, A:L.161 01.5: 21 residues within 4Å: Chain A: Y.68, L.210 Chain B: Q.20, C.23, G.24, S.25, C.26, W.27, S.59, E.60, N.61, D.62, G.65, G.66, G.67, Y.68, M.69, A.135, L.161, N.162, H.163 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:D.62, B:Y.68, B:A.135 Hydrogen bonds: B:Q.20, B:C.26, B:G.67, B:N.162 Halogen bonds: B:Y.68

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

PGE.2: 4 residues within 4Å: Chain A: Y.68, L.161 Chain B: Y.68 Ligands: 01.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.68, B:Y.68 PGE.3: 5 residues within 4Å: Chain A: R.9, N.191, K.192, Y.194, L.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.9, A:R.9 PGE.9: 9 residues within 4Å: Chain A: E.116 Chain B: V.55, D.56, C.57, V.58, S.59, D.62, G.63, E.94 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.94, A:E.116 Water bridges: B:V.58, B:D.62

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: D.153, E.154, S.155 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.155 CA.6: 6 residues within 4Å: Chain A: E.60, N.71, Q.74 Chain B: E.60, N.71, Q.74 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.60, B:E.60, A:E.60, A:E.60 CA.7: 1 residues within 4Å: Chain B: E.116 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.116, H2O.3, H2O.3, H2O.13, H2O.15 CA.8: 1 residues within 4Å: Chain B: S.59 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.59, H2O.4, H2O.8, H2O.10, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gourag, D. et al., Peptide-Small Molecule Hybrids as Novel Selective Irreversible Cathepsin-K Inhibitors in Primary Osteoclasts and Human Lung Cancer Tissue. To Be Published

Release Date

2025-07-30

Peptides

Cathepsin K: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cathepsin K