SMTL ID : 8w7e.1

Design, synthesis and biological evaluations of novel small molecular hyper-activators of human caseinolytic peptidase P (hClpP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-14-mer

Ligands

14 x 9I3: 3-[(3-chlorophenyl)methyl]-6-[(4-chlorophenyl)methyl]-2,4-dihydro-1H-pyrido[2,3-c][2,7]naphthyridin-5-one

9I3.1: 15 residues within 4Å: Chain A: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 Chain B: I.46, L.50, F.51, S.54, T.81, Y.84 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.25, A:E.28, A:I.30, A:Y.64, A:L.116, B:L.50, B:L.50 pi-Stacking: A:H.62, B:Y.84 9I3.2: 13 residues within 4Å: Chain B: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94 Chain F: L.50, F.51, S.54, T.81, Y.84 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain F Hydrophobic interactions: B:E.28, B:I.30, B:Y.64, F:L.50, F:L.50 Hydrogen bonds: B:Y.64 pi-Stacking: F:Y.84 9I3.3: 15 residues within 4Å: Chain C: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 Chain D: I.46, L.50, F.51, S.54, T.81, Y.84 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:E.28, C:I.30, C:Y.64, C:L.116, D:I.46, D:L.50, D:L.50, D:T.81 Hydrogen bonds: C:Y.64 pi-Stacking: C:H.62, D:Y.84 9I3.4: 14 residues within 4Å: Chain D: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 Chain G: L.50, F.51, S.54, T.81, Y.84 12 PLIP interactions: 8 interactions with chain D, 4 interactions with chain G Hydrophobic interactions: D:L.25, D:E.28, D:I.30, D:Y.64, D:L.116, G:L.50, G:L.50, G:T.81 Hydrogen bonds: D:E.28, D:Y.64 pi-Stacking: D:H.62, G:Y.84 9I3.5: 15 residues within 4Å: Chain A: I.46, L.50, F.51, S.54, T.81, Y.84 Chain E: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 12 PLIP interactions: 7 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:L.25, E:E.28, E:I.30, E:Y.64, E:L.116, A:L.50, A:L.50, A:T.81 Hydrogen bonds: E:E.28, A:Q.53 pi-Stacking: E:H.62, A:Y.84 9I3.6: 12 residues within 4Å: Chain F: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94 Chain I: L.50, F.51, S.54, T.81 10 PLIP interactions: 4 interactions with chain I, 6 interactions with chain F Hydrophobic interactions: I:L.50, I:L.50, F:L.25, F:E.28, F:I.30, F:Y.64 Hydrogen bonds: I:Q.53, F:Y.64 pi-Stacking: I:Y.84, F:H.62 9I3.7: 13 residues within 4Å: Chain G: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 Chain J: L.50, F.51, S.54, Y.84 10 PLIP interactions: 2 interactions with chain J, 8 interactions with chain G Hydrophobic interactions: J:L.50, G:L.25, G:E.28, G:I.30, G:I.30, G:Y.64, G:V.94, G:L.116 pi-Stacking: J:Y.84, G:H.62 9I3.8: 13 residues within 4Å: Chain E: L.50, F.51, S.54, T.81, Y.84 Chain H: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94 8 PLIP interactions: 5 interactions with chain H, 3 interactions with chain E Hydrophobic interactions: H:L.25, H:E.28, H:I.30, H:Y.64, E:L.50, E:L.50 pi-Stacking: H:H.62, E:Y.84 9I3.9: 15 residues within 4Å: Chain I: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94, L.116 Chain K: I.46, L.50, F.51, S.54, T.81, Y.84 8 PLIP interactions: 2 interactions with chain K, 6 interactions with chain I Hydrophobic interactions: K:L.50, I:E.28, I:I.30, I:Y.64, I:L.116 pi-Stacking: K:Y.84, I:H.62 Hydrogen bonds: I:Y.64 9I3.10: 14 residues within 4Å: Chain J: R.24, L.25, E.28, H.62, Y.64, W.92, V.94, L.116 Chain M: L.50, F.51, Q.53, S.54, T.81, Y.84 7 PLIP interactions: 4 interactions with chain J, 3 interactions with chain M Hydrophobic interactions: J:E.28, J:W.92, M:L.50, M:L.50 pi-Stacking: J:H.62, J:Y.64 Hydrogen bonds: M:Y.84 9I3.11: 14 residues within 4Å: Chain H: I.46, L.50, F.51, S.54, T.81, Y.84 Chain K: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94 11 PLIP interactions: 4 interactions with chain H, 7 interactions with chain K Hydrophobic interactions: H:I.46, H:L.50, H:T.81, K:L.25, K:E.28, K:I.30, K:W.92 pi-Stacking: H:Y.84, K:H.62, K:Y.64 Hydrogen bonds: K:E.28 9I3.12: 13 residues within 4Å: Chain L: 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, L.116 10 PLIP interactions: 7 interactions with chain M, 3 interactions with chain L Hydrophobic interactions: M:E.28, M:E.28, M:I.30, M:Y.64, M:W.92, M:L.116, L:L.50, L:Y.84 Hydrogen bonds: M:E.28 pi-Stacking: L:Y.84 9I3.13: 14 residues within 4Å: Chain C: L.50, F.51, Q.53, S.54, T.81, Y.84 Chain N: R.24, L.25, E.28, I.30, H.62, Y.64, W.92, V.94 8 PLIP interactions: 4 interactions with chain N, 4 interactions with chain C Hydrophobic interactions: N:I.30, N:Y.64, C:L.50, C:T.81 Hydrogen bonds: N:Y.64, C:Q.53 pi-Stacking: N:H.62, C:Y.84 9I3.14: 14 residues within 4Å: Chain L: R.24, L.25, E.28, H.62, Y.64, W.92, V.94 Chain N: I.46, L.50, F.51, Q.53, S.54, T.81, Y.84 9 PLIP interactions: 5 interactions with chain N, 4 interactions with chain L Hydrophobic interactions: N:I.46, N:L.50, N:L.50, L:L.25, L:E.28, L:Y.64 Hydrogen bonds: N:Q.53 pi-Stacking: N:Y.84, L:H.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, J.-X. et al., Design, synthesis and biological evaluations of novel small molecular hyper-activators of human caseinolytic peptidase P (hClpP). 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
B

C
C

D
D

E
F

F
G

G
H

H
I

I
K

J
M

K
N

L
J

M
L

N
E

ATP-dependent Clp protease proteolytic subunit, mitochondrial

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