SMTL ID : 6qbs.1

The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

HVW.1: 22 residues within 4Å: Chain A: Q.19, G.23, C.25, W.26, E.59, N.60, D.61, G.64, G.65, G.66, Y.67, M.68, A.134, I.135, L.160, N.161, H.162, A.163, W.184, L.209 Chain B: Y.67, L.209 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.61, A:Y.67, A:A.163 Hydrogen bonds: A:G.66, A:N.161 Halogen bonds: A:Y.67, A:L.160 HVW.4: 22 residues within 4Å: Chain A: Y.67, L.209 Chain B: Q.19, G.23, S.24, C.25, W.26, E.59, N.60, D.61, G.64, G.65, G.66, Y.67, M.68, A.134, L.160, N.161, H.162, A.163, W.184, L.209 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:D.61, B:Y.67, B:A.134, B:A.163 Hydrogen bonds: B:G.66, B:N.161 Water bridges: B:H.162 Halogen bonds: B:Y.67

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.59, N.70, Q.73 Chain B: E.59, N.70, Q.73 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.59, A:E.59, B:E.59, B:E.59

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

CL.3: 4 residues within 4Å: Chain A: K.122, K.176, R.198, N.199 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: K.122, K.176, R.198, N.199 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mons, E. et al., The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K. J. Am. Chem. Soc. (2019)

Release Date

2019-02-06

Peptides

Cathepsin K: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cathepsin K

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