SMTL ID : 6dl7.1

Human mitochondrial ClpP in complex with ONC201 (TIC10)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-heptamer

Ligands

7 x ONC: 7-benzyl-4-[(2-methylphenyl)methyl]-6,7,8,9-tetrahydroimidazo[1,2-a]pyrido[3,4-e]pyrimidin-5(4H)-one(Non-covalent)

ONC.1: 13 residues within 4Å: Chain A: L.23, E.26, I.28, H.60, Y.62, W.90, L.114 Chain G: I.44, L.48, F.49, S.52, T.79, Y.82 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain G Hydrophobic interactions: A:L.23, A:E.26, A:I.28, A:Y.62, A:W.90, A:L.114, G:I.44, G:L.48 Hydrogen bonds: A:E.26 pi-Stacking: A:H.60, G:Y.82 ONC.2: 12 residues within 4Å: Chain A: I.44, L.48, F.49, S.52, T.79, Y.82 Chain B: L.23, E.26, H.60, Y.62, W.90, L.114 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.23, B:E.26, B:Y.62, B:W.90, B:L.114, A:I.44, A:L.48, A:L.48 Hydrogen bonds: B:E.26 pi-Stacking: B:H.60, A:Y.82 Water bridges: A:Q.51, A:Q.51 ONC.3: 14 residues within 4Å: Chain B: I.44, L.48, F.49, S.52, T.79, Y.82 Chain C: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.23, C:E.26, C:I.28, C:Y.62, C:Y.62, C:W.90, C:L.114, B:I.44, B:L.48, B:L.48 Hydrogen bonds: C:E.26, C:Y.62 pi-Stacking: C:H.60, B:Y.82 Water bridges: B:Y.82 ONC.4: 14 residues within 4Å: Chain C: I.44, L.48, F.49, S.52, T.79, Y.82 Chain D: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:I.44, C:L.48, C:L.48, D:L.23, D:E.26, D:I.28, D:Y.62, D:W.90, D:L.114 Water bridges: C:Q.51 pi-Stacking: C:Y.82, D:H.60 Hydrogen bonds: D:Y.62 ONC.5: 11 residues within 4Å: Chain D: L.48, F.49, S.52, T.79, Y.82 Chain E: L.23, E.26, I.28, H.60, Y.62, W.90 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:L.48, E:L.23, E:E.26, E:I.28, E:Y.62 Water bridges: D:Q.51, D:Q.51 pi-Stacking: D:Y.82, E:H.60 Hydrogen bonds: E:Y.62 ONC.6: 14 residues within 4Å: Chain E: I.44, L.48, S.52, T.79, Y.82 Chain F: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 15 PLIP interactions: 10 interactions with chain F, 5 interactions with chain E Hydrophobic interactions: F:L.23, F:E.26, F:I.28, F:Y.62, F:Y.62, F:W.90, F:V.92, F:L.114, E:I.44, E:L.48, E:L.48 Hydrogen bonds: F:Y.62 pi-Stacking: F:H.60, E:Y.82 Water bridges: E:Q.51 ONC.7: 13 residues within 4Å: Chain F: I.44, L.48, F.49, S.52, T.79, Y.82 Chain G: L.23, E.26, I.28, H.60, Y.62, W.90, V.92 11 PLIP interactions: 4 interactions with chain F, 7 interactions with chain G Hydrophobic interactions: F:I.44, F:L.48, G:L.23, G:E.26, G:Y.62, G:Y.62, G:V.92 Water bridges: F:Q.51 pi-Stacking: F:Y.82, G:H.60 Hydrogen bonds: G:E.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishizawa, J. et al., Mitochondrial ClpP-Mediated Proteolysis Induces Selective Cancer Cell Lethality. Cancer Cell (2019)

Release Date

2019-05-08

Peptides

ATP-dependent Clp protease proteolytic subunit, mitochondrial: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ATP-dependent Clp protease proteolytic subunit, mitochondrial

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