SMTL ID : 8i7x.1

Crystal structure of human ClpP in complex with ZG36

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-14-mer

Ligands

14 x OSR: (6S,9aS)-N-[(4-bromophenyl)methyl]-6-[(2S)-butan-2-yl]-8-[(4-methoxynaphthalen-1-yl)methyl]-4,7-bis(oxidanylidene)-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide(Non-covalent)

OSR.1: 17 residues within 4Å: Chain B: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain C: I.19, R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 16 PLIP interactions: 7 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:I.44, B:L.48, B:L.48, B:F.49, B:Y.82, B:Y.82, C:R.22, C:L.23, C:E.26, C:I.28, C:Y.62, C:L.114 Hydrogen bonds: B:Y.82, C:E.26, C:E.26 Halogen bonds: C:I.19 OSR.2: 18 residues within 4Å: Chain A: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain B: I.19, R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114, P.192 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:R.22, B:L.23, B:E.26, B:I.28, B:Y.62, B:L.114, B:P.192, A:I.44, A:L.48, A:L.48, A:L.48, A:F.49, A:Y.82, A:Y.82 Hydrogen bonds: B:E.26, B:E.26, A:Y.82 Halogen bonds: B:I.19 OSR.3: 16 residues within 4Å: Chain C: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain D: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.23, D:E.26, D:I.28, D:Y.62, D:Y.62, D:V.92, D:L.114, C:I.44, C:L.48, C:L.48, C:Y.82 OSR.4: 17 residues within 4Å: Chain D: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain E: I.19, R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 13 PLIP interactions: 6 interactions with chain D, 7 interactions with chain E Hydrophobic interactions: D:I.44, D:L.48, D:L.48, D:F.49, D:Y.82, D:Y.82, E:L.23, E:E.26, E:I.28, E:Y.62, E:L.114 Hydrogen bonds: E:E.26 Halogen bonds: E:I.19 OSR.5: 17 residues within 4Å: Chain E: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain F: I.19, R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 15 PLIP interactions: 6 interactions with chain E, 9 interactions with chain F Hydrophobic interactions: E:I.44, E:L.48, E:L.48, E:F.49, E:Y.82, E:Y.82, F:R.22, F:L.23, F:E.26, F:I.28, F:Y.62, F:L.114 Hydrogen bonds: F:E.26 pi-Stacking: F:W.90 Halogen bonds: F:I.19 OSR.6: 17 residues within 4Å: Chain A: I.19, R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 Chain G: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain G Hydrophobic interactions: A:L.23, A:E.26, A:I.28, A:Y.62, A:L.114, G:I.44, G:L.48, G:L.48, G:L.48, G:F.49, G:Y.82, G:Y.82 Hydrogen bonds: A:E.26, A:E.26 pi-Stacking: A:W.90 Halogen bonds: A:I.19 OSR.7: 14 residues within 4Å: Chain F: I.44, L.48, F.49, Q.51, S.52, Y.82 Chain G: I.19, R.22, L.23, E.26, I.28, H.60, Y.62, W.90 11 PLIP interactions: 5 interactions with chain F, 6 interactions with chain G Hydrophobic interactions: F:I.44, F:L.48, F:F.49, F:Y.82, F:Y.82, G:L.23, G:E.26, G:I.28, G:Y.62 Hydrogen bonds: G:E.26 Halogen bonds: G:I.19 OSR.8: 16 residues within 4Å: Chain H: I.19, R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 Chain N: I.44, L.48, F.49, Q.51, S.52, T.79, Y.82 17 PLIP interactions: 9 interactions with chain H, 8 interactions with chain N Hydrophobic interactions: H:R.22, H:L.23, H:E.26, H:I.28, H:Y.62, H:L.114, N:I.44, N:L.48, N:L.48, N:L.48, N:F.49, N:Y.82, N:Y.82 Hydrogen bonds: H:E.26, H:E.26, N:Y.82 Halogen bonds: H:I.19 OSR.9: 17 residues within 4Å: Chain H: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain I: I.19, R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 16 PLIP interactions: 9 interactions with chain I, 7 interactions with chain H Hydrophobic interactions: I:R.22, I:L.23, I:E.26, I:I.28, I:Y.62, I:L.114, H:I.44, H:L.48, H:L.48, H:F.49, H:Y.82, H:Y.82 Hydrogen bonds: I:E.26, I:E.26, H:Y.82 Halogen bonds: I:I.19 OSR.10: 17 residues within 4Å: Chain I: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain J: I.19, R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 14 PLIP interactions: 9 interactions with chain J, 5 interactions with chain I Hydrophobic interactions: J:R.22, J:L.23, J:E.26, J:I.28, J:Y.62, J:L.114, I:I.44, I:L.48, I:F.49, I:Y.82 Hydrogen bonds: J:E.26, I:Y.82 pi-Stacking: J:W.90 Halogen bonds: J:I.19 OSR.11: 18 residues within 4Å: Chain K: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain L: I.19, L.23, E.26, I.28, H.60, Y.62, W.90, V.92, L.114, P.192 15 PLIP interactions: 6 interactions with chain K, 9 interactions with chain L Hydrophobic interactions: K:I.44, K:L.48, K:L.48, K:F.49, K:Y.82, K:Y.82, L:L.23, L:E.26, L:I.28, L:Y.62, L:V.92, L:L.114, L:P.192 Hydrogen bonds: L:E.26 Halogen bonds: L:I.19 OSR.12: 16 residues within 4Å: Chain J: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain K: R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 14 PLIP interactions: 8 interactions with chain J, 6 interactions with chain K Hydrophobic interactions: J:I.44, J:L.48, J:L.48, J:F.49, J:Q.51, J:Y.82, J:Y.82, K:L.23, K:E.26, K:I.28, K:Y.62, K:L.114 Hydrogen bonds: J:Y.82, K:E.26 OSR.13: 17 residues within 4Å: Chain L: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain M: I.19, R.22, L.23, E.26, I.28, H.60, Y.62, W.90, L.114 15 PLIP interactions: 6 interactions with chain L, 9 interactions with chain M Hydrophobic interactions: L:I.44, L:L.48, L:L.48, L:L.48, L:F.49, L:Y.82, M:R.22, M:L.23, M:E.26, M:I.28, M:I.28, M:Y.62, M:L.114 Hydrogen bonds: M:E.26 Halogen bonds: M:I.19 OSR.14: 17 residues within 4Å: Chain M: I.44, A.45, L.48, F.49, Q.51, S.52, T.79, Y.82 Chain N: I.19, R.22, L.23, E.26, I.28, H.60, Y.62, W.90, P.192 15 PLIP interactions: 7 interactions with chain M, 8 interactions with chain N Hydrophobic interactions: M:I.44, M:L.48, M:L.48, M:F.49, M:Y.82, M:Y.82, N:L.23, N:E.26, N:I.28, N:Y.62, N:P.192 Hydrogen bonds: M:Y.82, N:E.26, N:E.26 Halogen bonds: N:I.19

Links

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Citation

Zhang, R. et al., Assessment of the structure-activity relationship and antileukemic activity of diacylpyramide compounds as human ClpP agonists. Eur.J.Med.Chem. (2023)

Release Date

2023-07-19

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
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

ATP-dependent Clp protease proteolytic subunit, mitochondrial

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