SMTL ID : 8rnd.1

Cathepsin S in complex with NNPI-C10 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: D.128, K.131, E.184, R.206, N.207 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.131, A:R.206, A:N.207, A:N.207 Water bridges: A:R.206 EDO.3: 5 residues within 4Å: Chain A: Q.43, L.46, K.47, E.222, I.223 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.223, A:I.223, A:I.223 Water bridges: A:E.222 EDO.4: 4 residues within 4Å: Chain A: K.23, Y.24, F.34, Y.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.24 EDO.8: 3 residues within 4Å: Chain A: Y.24, G.26, S.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.24, A:Y.24

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

PGE.2: 9 residues within 4Å: Chain A: Y.124, G.125, R.126, E.127, Q.166, N.207, K.208, G.209, N.210 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.166, A:G.209, A:N.210

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 5 residues within 4Å: Chain A: V.158, Y.160, K.183, A.205, K.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.183, A:K.208

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: Y.160, C.164, T.165, Q.166, K.208, G.209, N.210, H.211, C.212, G.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.211, A:C.212 Water bridges: A:C.164

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 4 residues within 4Å: Chain A: K.99, Q.103, K.104, Q.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.103, A:Q.103, A:K.104, A:Q.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petruzzella, A. et al., Antibody-peptide conjugates deliver covalent inhibitors blocking oncogenic cathepsins. Nat.Chem.Biol. (2024)

Release Date

2024-06-05

Peptides

Cathepsin S: A
NNPI-C10 inhibitor: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cathepsin S

NNPI-C10 inhibitor

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