SMTL ID : 9k2k.1

Structure of ClpP from Staphylococcus aureus in complex with ZY7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 Å

Oligo State

homo-14-mer

Ligands

14 x 01: (6~{S},9~{a}~{S})-6-(2-methylpropyl)-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-~{N}-(phenylmethyl)-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-carboxamide

01.1: 13 residues within 4Å: Chain A: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain B: L.49, F.50, A.53, H.83 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.24, A:D.27, A:I.29, A:I.29, A:Y.61, A:Y.63, A:I.93, B:L.49, B:L.49, B:L.49, B:F.50, B:A.53 Hydrogen bonds: A:D.27, A:D.27 01.2: 14 residues within 4Å: Chain B: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain C: L.49, F.50, Q.52, A.53, H.83 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.24, B:I.29, B:I.29, B:Y.61, B:Y.63, B:I.93, C:L.49, C:L.49, C:L.49, C:F.50, C:A.53 Hydrogen bonds: B:D.27, B:D.27 01.3: 13 residues within 4Å: Chain C: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain D: L.49, F.50, Q.52, A.53 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:L.49, D:L.49, D:A.53, C:L.24, C:D.27, C:I.29, C:I.29, C:Y.61, C:Y.63, C:I.93 Hydrogen bonds: C:D.27, C:D.27 01.4: 14 residues within 4Å: Chain D: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain E: L.49, F.50, Q.52, A.53, H.83 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:L.24, D:D.27, D:I.29, D:I.29, D:Y.61, D:Y.63, D:Y.63, D:I.93, E:L.49, E:F.50, E:A.53 Hydrogen bonds: D:D.27, D:D.27 01.5: 14 residues within 4Å: Chain E: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain F: L.49, F.50, Q.52, A.53, H.83 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:L.24, E:I.29, E:I.29, E:Y.61, E:Y.63, E:I.93, F:L.49, F:L.49, F:F.50, F:A.53 Hydrogen bonds: E:D.27, E:D.27, E:Q.89 01.6: 15 residues within 4Å: Chain F: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, L.115, M.190 Chain G: V.45, L.49, F.50, A.53, H.83 14 PLIP interactions: 9 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: F:L.24, F:D.27, F:I.29, F:Y.61, F:Y.63, F:I.93, F:L.115, G:V.45, G:L.49, G:L.49, G:F.50, G:A.53 Hydrogen bonds: F:D.27, F:D.27 01.7: 13 residues within 4Å: Chain A: L.49, F.50, A.53, H.83 Chain G: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 13 PLIP interactions: 8 interactions with chain G, 5 interactions with chain A Hydrophobic interactions: G:L.24, G:I.29, G:Y.61, G:Y.63, G:I.93, A:L.49, A:L.49, A:L.49, A:F.50, A:A.53 Hydrogen bonds: G:D.27, G:D.27, G:Q.89 01.8: 14 residues within 4Å: Chain H: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain I: L.49, F.50, Q.52, A.53, H.83 12 PLIP interactions: 6 interactions with chain I, 6 interactions with chain H Hydrophobic interactions: I:L.49, I:L.49, I:L.49, I:F.50, I:F.50, I:A.53, H:L.24, H:I.29, H:Y.61, H:Y.63, H:I.93 Hydrogen bonds: H:D.27 01.9: 14 residues within 4Å: Chain I: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain J: L.49, F.50, Q.52, A.53, H.83 12 PLIP interactions: 7 interactions with chain I, 5 interactions with chain J Hydrophobic interactions: I:L.24, I:D.27, I:I.29, I:Y.61, I:Y.63, I:I.93, J:L.49, J:L.49, J:L.49, J:F.50, J:A.53 Hydrogen bonds: I:D.27 01.10: 14 residues within 4Å: Chain J: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190, E.193 Chain K: L.49, F.50, A.53, H.83 11 PLIP interactions: 7 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: J:L.24, J:I.29, J:I.29, J:Y.61, J:Y.63, J:I.93, K:L.49, K:L.49, K:F.50, K:A.53 Hydrogen bonds: J:D.27 01.11: 15 residues within 4Å: Chain K: R.23, L.24, D.27, I.29, Y.61, I.91, I.93, L.115, M.190, E.193 Chain L: L.49, F.50, Q.52, A.53, H.83 12 PLIP interactions: 8 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: K:L.24, K:D.27, K:I.29, K:I.29, K:Y.61, K:I.93, K:L.115, L:L.49, L:L.49, L:F.50, L:A.53 Hydrogen bonds: K:D.27 01.12: 14 residues within 4Å: Chain L: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, M.190 Chain M: V.45, L.49, F.50, A.53 15 PLIP interactions: 9 interactions with chain L, 6 interactions with chain M Hydrophobic interactions: L:L.24, L:D.27, L:I.29, L:Y.61, L:Y.63, L:Y.63, L:I.93, M:V.45, M:L.49, M:L.49, M:F.50, M:F.50, M:A.53 Hydrogen bonds: L:D.27, L:Q.89 01.13: 16 residues within 4Å: Chain M: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain N: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 15 PLIP interactions: 9 interactions with chain M, 6 interactions with chain N Hydrophobic interactions: M:L.24, M:D.27, M:I.29, M:I.29, M:Y.61, M:Y.63, M:Y.63, M:I.93, N:V.45, N:L.49, N:L.49, N:F.50, N:A.53, N:T.80 Hydrogen bonds: M:D.27 01.14: 15 residues within 4Å: Chain H: L.49, F.50, Q.52, A.53, H.83 Chain N: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190, E.193 11 PLIP interactions: 4 interactions with chain H, 7 interactions with chain N Hydrophobic interactions: H:L.49, H:L.49, H:F.50, H:A.53, N:L.24, N:I.29, N:I.29, N:Y.61, N:Y.63, N:I.93 Hydrogen bonds: N:D.27

Links

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Citation

Zhang, T. et al., Structure-Guided Development of ClpP Agonists with Potent Therapeutic Activities against Staphylococcus aureus Infection. J.Med.Chem. (2025)

Release Date

2025-02-19

Peptides

ATP-dependent Clp protease proteolytic subunit: 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

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