SMTL ID : 4x6j.1

Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: S.58 Ligands: CL.2 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: S.95, C.96 Ligands: GOL.1 Ligand excluded by PLIP

1 x K: POTASSIUM ION(Non-covalent)

K.3: 3 residues within 4Å: Chain A: M.196, A.197, A.203 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.197, A:A.203, H2O.6

3 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.4: 4 residues within 4Å: Chain A: R.8, N.190, Y.193, L.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.8, A:R.8 PGO.5: 6 residues within 4Å: Chain A: R.8, V.13, T.14, P.15, V.16, Y.193 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.8 Hydrogen bonds: A:T.14, A:V.16, A:Y.193 PGO.6: 3 residues within 4Å: Chain A: P.88, Y.89, V.90 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.88, A:V.90 Hydrogen bonds: A:Y.89

1 x 3Y2: 2-amino-4-chloro-N-(1-{[(2E)-2-iminoethyl]carbamoyl}cyclohexyl)benzamide(Covalent)

3Y2.7: 14 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, W.26, E.59, G.64, G.65, G.66, Y.67, A.134, L.160, N.161, H.162 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.134 Hydrogen bonds: A:C.25, A:G.66, A:G.66, A:N.161 Water bridges: A:Q.19, A:Q.19, A:G.64, A:G.64, A:H.162, A:H.162 pi-Stacking: A:Y.67 Halogen bonds: A:E.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borisek, J. et al., Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. J.Med.Chem. (2015)

Release Date

2015-09-09

Peptides

Cathepsin K: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cathepsin K

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