SMTL ID : 7qbo.1

Structure of the activation intermediate of cathepsin K in complex with the azadipeptide nitrile inhibitor Gu1303

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 9ZG: (phenylmethyl) ~{N}-[(2~{S})-1-[[aminomethyl(methyl)amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]carbamate(Non-covalent)

9ZG.1: 17 residues within 4Å: Chain A: Q.20, G.24, S.25, C.26, W.27, E.60, N.61, D.62, G.66, G.67, Y.68, A.135, L.161, N.162, H.163, A.164, L.210 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.62, A:Y.68, A:Y.68, A:Y.68, A:Y.68, A:A.135, A:L.161, A:A.164, A:L.210 Hydrogen bonds: A:Q.20, A:C.26, A:G.67, A:G.67 Water bridges: A:C.23, A:H.163

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

EDO.2: 5 residues within 4Å: Chain A: Y.152, D.153, E.154 Chain B: V.53, H.54 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.154, B:V.53, B:H.54 Water bridges: A:S.155 EDO.3: 6 residues within 4Å: Chain A: T.70, E.113, I.114, L.210, A.211, S.212 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.113, A:I.114, A:I.114, A:A.211 Water bridges: A:T.70, A:S.212 EDO.4: 4 residues within 4Å: Chain A: Q.20, G.21, W.185 Chain B: V.71 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.71, A:G.21

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

CL.5: 3 residues within 4Å: Chain A: Y.68, M.69, T.70 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: T.141 Chain B: S.68, E.69 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:T.141, B:S.68, H2O.6, H2O.8, H2O.9, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benysek, J. et al., Highly potent inhibitors of cathepsin K with a differently positioned cyanohydrazide warhead: structural analysis of binding mode to mature and zymogen-like enzymes. J Enzyme Inhib Med Chem (2022)

Release Date

2022-01-26

Peptides

Cathepsin K: A
Cathepsin K: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
P

Cathepsin K

Cathepsin K

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