SMTL ID : 8pi3.1

Cathepsin S Y132D mutant in complex with NNPI-C10 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-1-1-mer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: D.141, R.143, N.165 Ligands: CD.9 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: H.190 Ligands: CD.8 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain A: V.18, K.19, D.20, G.189, H.190 Ligands: CD.8 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain A: Q.21, C.27, H.166, W.188 Chain B: W.10 Ligands: CD.7 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain A: R.143, N.165 Chain B: X.7, W.10 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: K.41, G.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.41, A:G.45

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

EDO.5: 9 residues within 4Å: Chain A: C.160, T.161, Q.162, K.204, G.205, N.206, H.207, C.208, G.209 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.160, A:G.205, A:H.207, A:C.208 Water bridges: A:C.160 EDO.6: 5 residues within 4Å: Chain A: Q.39, L.42, K.43, E.218, I.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.219 EDO.13: 6 residues within 4Å: Chain A: Q.78, I.81, S.113, K.114, Y.115 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.115 EDO.16: 4 residues within 4Å: Chain A: Y.115, T.116, E.117 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.115, A:E.117 EDO.17: 4 residues within 4Å: Chain A: K.19, D.20, F.30, Y.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.20 Water bridges: A:Y.94

4 x CD: CADMIUM ION(Non-covalent)

CD.7: 8 residues within 4Å: Chain A: Q.21, C.27, H.166, G.167, W.188 Chain B: X.7, W.10 Ligands: CL.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.27, A:H.166, H2O.3 CD.8: 3 residues within 4Å: Chain A: H.190 Ligands: CL.2, CL.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.190 CD.9: 6 residues within 4Å: Chain A: D.141, R.143, H.144, C.160, T.161 Ligands: CL.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.141, A:D.141, A:H.144, H2O.2 CD.10: 2 residues within 4Å: Chain A: E.17, H.190 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.17, A:E.17, H2O.1

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

ACT.12: 3 residues within 4Å: Chain A: R.10, E.11 Ligands: PEG.19 No protein-ligand interaction detected (PLIP) ACT.14: 7 residues within 4Å: Chain A: R.143, N.163, V.164, N.165 Chain B: H.4, V.8, M.9 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:M.9 Hydrogen bonds: A:N.165 Salt bridges: A:R.143

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

PEG.15: 5 residues within 4Å: Chain A: D.20, G.22, S.23, F.148, W.188 No protein-ligand interaction detected (PLIP) PEG.18: 7 residues within 4Å: Chain A: D.5, K.127, Y.173, D.175, E.180, R.202, N.203 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.127, A:R.202, A:R.202, A:N.203 Water bridges: A:G.174, A:D.175 PEG.19: 9 residues within 4Å: Chain A: R.10, V.15, T.16, E.17, V.18, L.47, K.185, Y.197 Ligands: ACT.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.15, A:T.16, A:V.18, A:Y.197

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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