SMTL ID : 9k2d.1

Structure of ClpP from Staphylococcus aureus in complex with ZY39

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-14-mer

Ligands

14 x 01: (6~{S},9~{a}~{S})-6-[(2~{S})-butan-2-yl]-8-[(4-methoxynaphthalen-1-yl)methyl]-4,7-bis(oxidanylidene)-~{N}-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-carboxamide

01.1: 16 residues within 4Å: Chain A: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 Chain G: V.45, S.46, L.49, F.50, A.53, H.83 12 PLIP interactions: 2 interactions with chain G, 10 interactions with chain A Hydrophobic interactions: G:L.49, G:A.53, A:D.27, A:I.29, A:Y.61, A:Y.63, A:I.91, A:I.91, A:I.93 Water bridges: A:D.27, A:D.27 Halogen bonds: A:R.23 01.3: 16 residues within 4Å: Chain A: V.45, S.46, L.49, F.50, A.53, H.83 Chain B: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, E.193 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:V.45, A:L.49, A:A.53, B:D.27, B:I.29, B:Y.61, B:Y.63, B:I.91, B:I.91, B:I.93 Water bridges: B:D.27, B:D.27 Halogen bonds: B:R.23 01.5: 16 residues within 4Å: Chain B: V.45, S.46, L.49, F.50, A.53, H.83 Chain C: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.29, C:Y.61, C:Y.63, C:I.91, C:I.91, C:I.93, B:A.53 Water bridges: C:Y.61 01.6: 16 residues within 4Å: Chain C: V.45, S.46, L.49, F.50, A.53, H.83 Chain D: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.29, D:Y.61, D:Y.63, D:I.91, D:I.91, D:I.93, C:L.49 Hydrogen bonds: D:D.27 Halogen bonds: D:R.23 01.8: 17 residues within 4Å: Chain D: V.45, S.46, L.49, F.50, A.53, H.83 Chain E: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190, E.193 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:I.29, E:Y.61, E:Y.63, E:I.93, D:L.49, D:A.53 Water bridges: E:D.27, E:D.27 Halogen bonds: E:R.23 01.11: 16 residues within 4Å: Chain E: V.45, S.46, L.49, F.50, A.53, H.83 Chain F: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 12 PLIP interactions: 3 interactions with chain E, 9 interactions with chain F Hydrophobic interactions: E:V.45, E:L.49, E:A.53, F:I.29, F:Y.61, F:Y.63, F:I.91, F:I.91, F:I.93 Hydrogen bonds: F:D.27, F:D.27 Halogen bonds: F:R.23 01.13: 15 residues within 4Å: Chain F: V.45, S.46, L.49, F.50, A.53 Chain G: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: G:D.27, G:I.29, G:Y.61, G:Y.63, G:I.91, G:I.91, G:I.93, F:A.53 Water bridges: G:D.27, G:D.27 Halogen bonds: G:R.23 Hydrogen bonds: F:Q.52 01.15: 17 residues within 4Å: Chain H: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190, E.193 Chain N: V.45, S.46, L.49, F.50, A.53, H.83 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain N Hydrophobic interactions: H:D.27, H:I.29, H:Y.61, H:Y.63, H:I.93, N:L.49, N:A.53 Hydrogen bonds: H:D.27 Halogen bonds: H:R.23 01.17: 16 residues within 4Å: Chain H: V.45, S.46, L.49, F.50, Q.52, A.53 Chain I: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 10 PLIP interactions: 9 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:D.27, I:I.29, I:Y.61, I:Y.63, I:I.91, I:I.91, I:I.93, H:A.53 Hydrogen bonds: I:D.27 Halogen bonds: I:R.23 01.19: 16 residues within 4Å: Chain I: V.45, S.46, L.49, F.50, A.53, H.83 Chain J: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 11 PLIP interactions: 10 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:I.29, J:I.29, J:Y.61, J:Y.63, J:I.91, J:I.91, J:I.93, I:V.45 Hydrogen bonds: J:D.27, J:D.27 Halogen bonds: J:R.23 01.21: 16 residues within 4Å: Chain J: V.45, S.46, L.49, F.50, A.53, H.83 Chain K: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:D.27, K:I.29, K:Y.61, K:Y.63, K:I.91, K:I.91, K:I.93 Hydrogen bonds: K:D.27, K:D.27 Halogen bonds: K:R.23 01.23: 16 residues within 4Å: Chain K: V.45, S.46, L.49, F.50, A.53, H.83 Chain L: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 12 PLIP interactions: 9 interactions with chain L, 3 interactions with chain K Hydrophobic interactions: L:I.29, L:Y.61, L:Y.63, L:I.91, L:I.91, L:I.93, K:V.45, K:L.49, K:A.53 Hydrogen bonds: L:D.27, L:D.27 Halogen bonds: L:R.23 01.25: 15 residues within 4Å: Chain L: V.45, S.46, L.49, F.50, A.53 Chain M: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 9 PLIP interactions: 8 interactions with chain M, 1 interactions with chain L Hydrophobic interactions: M:D.27, M:I.29, M:Y.61, M:Y.63, M:I.91, M:I.91, M:I.93, L:A.53 Halogen bonds: M:R.23 01.27: 16 residues within 4Å: Chain M: V.45, S.46, L.49, F.50, A.53, H.83 Chain N: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, I.93, M.190 11 PLIP interactions: 9 interactions with chain N, 2 interactions with chain M Hydrophobic interactions: N:I.29, N:Y.61, N:Y.63, N:I.91, N:I.91, N:I.93, M:L.49, M:A.53 Hydrogen bonds: N:D.27 Water bridges: N:Q.89 Halogen bonds: N:R.23

14 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 7 residues within 4Å: Chain A: S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.102, A:I.122, A:L.150 Hydrogen bonds: A:H.123, A:H.123 MPD.4: 9 residues within 4Å: Chain B: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.71, B:F.102, B:I.122, B:L.150 Hydrogen bonds: B:H.123, B:H.123 MPD.7: 8 residues within 4Å: Chain C: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.102, C:L.150, C:L.154 Hydrogen bonds: C:H.123, C:H.123 MPD.9: 8 residues within 4Å: Chain D: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.71, D:F.102, D:L.150 Hydrogen bonds: D:H.123, D:H.123 MPD.10: 9 residues within 4Å: Chain E: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:V.71, E:F.102, E:L.150, E:L.154 Hydrogen bonds: E:H.123, E:H.123 MPD.12: 9 residues within 4Å: Chain F: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:V.71, F:F.102, F:L.150 Hydrogen bonds: F:H.123, F:H.123 MPD.14: 8 residues within 4Å: Chain G: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:F.102, G:L.150, G:L.154 Hydrogen bonds: G:H.123, G:H.123 MPD.16: 9 residues within 4Å: Chain H: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:V.71, H:F.102, H:L.150, H:L.154 Hydrogen bonds: H:H.123, H:H.123 MPD.18: 9 residues within 4Å: Chain I: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, L.150, L.154 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:F.102, I:I.122, I:L.150 Hydrogen bonds: I:H.123, I:H.123 MPD.20: 8 residues within 4Å: Chain J: V.71, S.98, M.99, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:V.71, J:F.102, J:L.150, J:L.154 Hydrogen bonds: J:H.123, J:H.123 MPD.22: 9 residues within 4Å: Chain K: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:V.71, K:F.102, K:L.150, K:L.154 Hydrogen bonds: K:H.123, K:H.123 MPD.24: 9 residues within 4Å: Chain L: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:V.71, L:F.102, L:L.150, L:L.154 Hydrogen bonds: L:H.123, L:H.123 MPD.26: 10 residues within 4Å: Chain M: V.71, S.98, M.99, F.102, I.122, H.123, Q.124, P.125, L.150, L.154 6 PLIP interactions: 6 interactions with chain M Hydrophobic interactions: M:V.71, M:F.102, M:I.122, M:L.150, M:L.154 Hydrogen bonds: M:H.123 MPD.28: 8 residues within 4Å: Chain N: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:V.71, N:F.102, N:L.150 Hydrogen bonds: N:H.123, N:H.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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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