SMTL ID : 8w7c.1

Activation of mitochondrial Caseinolytic Protease P (ClpP) induces selective cancer cell lethality

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-14-mer

Ligands

14 x R89: 11-[(3-chlorophenyl)methyl]-7-[[4-(trifluoromethyl)phenyl]methyl]-2,5,7,11-tetrazatricyclo[7.4.0.0^{2,6}]trideca-1(9),3,5-trien-8-one(Non-covalent)

R89.1: 16 residues within 4Å: Chain A: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 Chain E: I.46, A.47, L.50, F.51, S.54, T.81, Y.84 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:I.46, E:L.50, E:T.81, A:L.25, A:E.28, A:L.116 pi-Stacking: E:Y.84, A:H.62 Halogen bonds: E:A.47 R89.2: 16 residues within 4Å: Chain B: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 Chain C: I.46, A.47, L.50, F.51, S.54, T.81, Y.84 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.50, C:T.81, B:L.25, B:E.28, B:Y.64, B:L.116 pi-Stacking: C:Y.84 Halogen bonds: C:A.47 Hydrogen bonds: B:E.28 R89.3: 15 residues within 4Å: Chain A: I.46, A.47, L.50, F.51, S.54, T.81, Y.84 Chain C: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94 12 PLIP interactions: 5 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:L.25, C:E.28, C:I.30, C:Y.64, C:W.92, A:I.46, A:L.50, A:L.50, A:T.81 Hydrogen bonds: A:Q.53 pi-Stacking: A:Y.84 Halogen bonds: A:A.47 R89.4: 17 residues within 4Å: Chain B: I.46, L.50, F.51, Q.53, S.54, D.80, T.81, Y.84 Chain D: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: D:L.25, D:E.28, D:I.30, D:Y.64, D:W.92, D:V.94, D:L.116, B:I.46, B:L.50 Hydrogen bonds: D:E.28, B:Q.53 pi-Stacking: D:Y.64 Halogen bonds: D:R.24, B:D.80 R89.5: 16 residues within 4Å: Chain E: R.24, L.25, E.28, I.30, M.34, H.62, Y.64, W.92, V.94, L.116 Chain F: I.46, L.50, F.51, S.54, T.81, Y.84 10 PLIP interactions: 4 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:L.116, F:I.46, F:L.50, F:L.50, F:L.50, F:T.81, F:Y.84 Hydrogen bonds: E:Y.64 pi-Stacking: E:H.62 Halogen bonds: E:R.24 R89.6: 15 residues within 4Å: Chain F: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94 Chain N: I.46, A.47, L.50, F.51, S.54, T.81, Y.84 9 PLIP interactions: 5 interactions with chain F, 4 interactions with chain N Hydrophobic interactions: F:L.25, F:E.28, F:Y.64, N:L.50 Hydrogen bonds: F:Y.64, N:Q.53 pi-Stacking: F:H.62, N:Y.84 Halogen bonds: N:A.47 R89.7: 16 residues within 4Å: Chain G: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 Chain K: I.46, A.47, L.50, F.51, S.54, T.81, Y.84 10 PLIP interactions: 5 interactions with chain K, 5 interactions with chain G Hydrophobic interactions: K:I.46, K:L.50, K:T.81, G:L.25, G:E.28, G:L.116 pi-Stacking: K:Y.84, G:H.62 Halogen bonds: K:A.47 Hydrogen bonds: G:E.28 R89.8: 16 residues within 4Å: Chain H: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 Chain I: I.46, A.47, L.50, F.51, S.54, T.81, Y.84 9 PLIP interactions: 5 interactions with chain H, 4 interactions with chain I Hydrophobic interactions: H:L.25, H:E.28, H:Y.64, H:L.116, I:L.50, I:T.81 Hydrogen bonds: H:Y.64 pi-Stacking: I:Y.84 Halogen bonds: I:A.47 R89.9: 15 residues within 4Å: Chain G: I.46, A.47, L.50, F.51, S.54, T.81, Y.84 Chain I: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94 13 PLIP interactions: 6 interactions with chain I, 7 interactions with chain G Hydrophobic interactions: I:L.25, I:E.28, I:I.30, I:Y.64, I:W.92, G:I.46, G:L.50, G:L.50, G:T.81 Hydrogen bonds: I:E.28, G:Q.53 pi-Stacking: G:Y.84 Halogen bonds: G:A.47 R89.10: 17 residues within 4Å: Chain H: I.46, L.50, F.51, Q.53, S.54, D.80, T.81, Y.84 Chain J: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 14 PLIP interactions: 10 interactions with chain J, 4 interactions with chain H Hydrophobic interactions: J:L.25, J:E.28, J:I.30, J:Y.64, J:W.92, J:V.94, J:L.116, H:I.46, H:L.50 Hydrogen bonds: J:Y.64, H:Q.53 pi-Stacking: J:Y.64 Halogen bonds: J:R.24, H:D.80 R89.11: 16 residues within 4Å: Chain K: R.24, L.25, E.28, I.30, M.34, H.62, Y.64, W.92, V.94, L.116 Chain L: I.46, L.50, F.51, S.54, T.81, Y.84 10 PLIP interactions: 7 interactions with chain L, 3 interactions with chain K Hydrophobic interactions: L:I.46, L:L.50, L:L.50, L:L.50, L:T.81, L:Y.84, K:L.116 Hydrogen bonds: L:Y.84 pi-Stacking: K:H.62 Halogen bonds: K:R.24 R89.12: 15 residues within 4Å: Chain L: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94 Chain M: I.46, A.47, L.50, F.51, S.54, T.81, Y.84 9 PLIP interactions: 5 interactions with chain L, 4 interactions with chain M Hydrophobic interactions: L:L.25, L:E.28, L:Y.64, M:L.50 Hydrogen bonds: L:E.28, M:Q.53 pi-Stacking: L:H.62, M:Y.84 Halogen bonds: M:A.47 R89.13: 13 residues within 4Å: Chain J: I.46, L.50, F.51, S.54, Y.84 Chain M: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94 8 PLIP interactions: 6 interactions with chain M, 2 interactions with chain J Hydrophobic interactions: M:L.25, M:E.28, M:Y.64, M:Y.64, M:W.92, J:L.50 pi-Stacking: M:H.62, J:Y.84 R89.14: 13 residues within 4Å: Chain D: I.46, L.50, F.51, S.54, Y.84 Chain N: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94 10 PLIP interactions: 8 interactions with chain N, 2 interactions with chain D Hydrophobic interactions: N:L.25, N:E.28, N:Y.64, N:Y.64, N:W.92, D:L.50 Hydrogen bonds: N:E.28, N:Y.64 pi-Stacking: N:H.62, D:Y.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, J.-X. et al., Activation of mitochondrial Caseinolytic Protease P (ClpP) induces selective cancer cell lethality. To Be Published

Release Date

2024-09-04

Peptides

ATP-dependent Clp protease proteolytic subunit, mitochondrial: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
E

E
F

F
G

G
A

H
C

I
D

J
E

K
F

L
G

M
B

N
B

ATP-dependent Clp protease proteolytic subunit, mitochondrial

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