SMTL ID : 7qbm.1

Structure of the activation intermediate of cathepsin K in complex with the 3-cyano-3-aza-beta-amino acid inhibitor Gu2602

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-1-1-mer

Ligands

1 x A0U: ~{tert}-butyl ~{N}-[iminomethyl-[2-[methyl-(phenylmethyl)amino]-2-oxidanylidene-ethyl]amino]carbamate(Covalent)

A0U.1: 12 residues within 4Å: Chain A: Q.20, G.24, S.25, C.26, W.27, G.65, G.66, G.67, L.161, N.162, H.163 Chain B: V.72 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.162 Hydrogen bonds: A:Q.20, A:C.26, A:G.67, A:N.162 Water bridges: A:H.163, A:H.163, A:H.163

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 1 residues within 4Å: Chain B: I.44 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.44

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.141 Chain B: S.68, E.69 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: B:S.68, A:T.141, H2O.5, H2O.6, H2O.8, H2O.9

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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