SMTL ID : 9k2b.1

Structure of ClpP from Staphylococcus aureus in complex with ZY18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-14-mer

Ligands

14 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: I.81, I.84, P.86 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:I.81, A:I.84, A:P.86, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain B: I.81, I.84, P.86 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:I.81, B:I.84, B:P.86, H2O.2, H2O.2 MG.7: 4 residues within 4Å: Chain C: I.81, I.84, K.85, P.86 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:I.81, C:I.84, C:P.86, H2O.3 MG.10: 4 residues within 4Å: Chain D: I.81, I.84, K.85, P.86 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:I.81, D:P.86, H2O.4 MG.14: 4 residues within 4Å: Chain E: I.81, I.84, K.85, P.86 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:I.81, E:I.84, E:P.86 MG.17: 3 residues within 4Å: Chain F: I.81, I.84, P.86 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:I.81, F:I.84, F:P.86, H2O.4, H2O.4 MG.20: 4 residues within 4Å: Chain G: I.81, I.84, K.85, P.86 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:I.81, G:I.84, G:P.86, H2O.5, H2O.5 MG.23: 3 residues within 4Å: Chain H: I.81, I.84, P.86 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:I.81, H:I.84, H:P.86, H2O.6, H2O.6 MG.26: 4 residues within 4Å: Chain I: I.81, I.84, K.85, P.86 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:I.81, I:I.84, I:P.86, H2O.6, H2O.7 MG.31: 4 residues within 4Å: Chain J: I.81, I.84, K.85, P.86 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:I.81, J:I.84, J:P.86, H2O.7, H2O.7 MG.34: 4 residues within 4Å: Chain K: I.81, I.84, K.85, P.86 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:I.81, K:I.84, K:P.86 MG.37: 3 residues within 4Å: Chain L: I.81, I.84, P.86 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:I.81, L:P.86 MG.39: 4 residues within 4Å: Chain M: I.81, Q.82, I.84, P.86 4 PLIP interactions: 3 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:I.81, M:I.84, M:P.86, H2O.8 MG.42: 3 residues within 4Å: Chain N: I.81, I.84, P.86 4 PLIP interactions: 3 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:I.81, N:I.84, N:P.86, H2O.9

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

MPD.2: 11 residues within 4Å: Chain A: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150, L.154, T.169 Ligand excluded by PLIP MPD.5: 9 residues within 4Å: Chain B: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.154 Ligand excluded by PLIP MPD.6: 4 residues within 4Å: Chain A: A.53 Chain B: E.9, R.23 Ligands: 01.3 Ligand excluded by PLIP MPD.8: 9 residues within 4Å: Chain C: V.71, S.98, M.99, S.101, I.122, H.123, Q.124, L.150, L.154 Ligand excluded by PLIP MPD.11: 9 residues within 4Å: Chain D: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, L.150, L.154 Ligand excluded by PLIP MPD.15: 7 residues within 4Å: Chain E: S.98, M.99, S.101, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.18: 7 residues within 4Å: Chain F: S.98, M.99, S.101, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.21: 7 residues within 4Å: Chain G: S.98, M.99, F.102, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.24: 11 residues within 4Å: Chain H: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150, L.154, T.169 Ligand excluded by PLIP MPD.27: 8 residues within 4Å: Chain I: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.28: 5 residues within 4Å: Chain H: A.53, Q.54 Chain I: E.9, R.23 Ligands: 01.29 Ligand excluded by PLIP MPD.32: 8 residues within 4Å: Chain J: S.98, M.99, S.101, I.122, H.123, L.150, L.154, T.169 Ligand excluded by PLIP MPD.35: 7 residues within 4Å: Chain K: S.98, M.99, S.101, I.122, H.123, L.150, L.154 Ligand excluded by PLIP MPD.38: 9 residues within 4Å: Chain L: S.98, M.99, S.101, I.122, H.123, Q.124, L.150, L.154, T.169 Ligand excluded by PLIP MPD.40: 8 residues within 4Å: Chain M: S.98, M.99, S.101, I.122, H.123, L.150, L.154, T.169 Ligand excluded by PLIP MPD.43: 6 residues within 4Å: Chain N: S.98, M.99, I.122, H.123, L.150, L.154 Ligand excluded by PLIP

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

01.3: 15 residues within 4Å: Chain A: L.49, F.50, Q.52, A.53, H.83 Chain B: R.23, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190, E.193 Ligands: MPD.6 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.49, A:L.49, A:F.50, B:D.27, B:I.29, B:Y.61, B:Y.63, B:Y.63, B:I.93 Hydrogen bonds: B:D.27 01.9: 14 residues within 4Å: Chain B: L.49, F.50, Q.52, A.53, H.83 Chain C: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.24, C:I.29, C:I.29, C:Y.61, C:Y.63, C:Y.63, C:I.91, C:I.93, B:L.49, B:L.49, B:F.50, B:A.53 Hydrogen bonds: C:D.27, C:D.27 01.12: 14 residues within 4Å: Chain C: L.49, F.50, Q.52, A.53, H.83 Chain D: R.23, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190, E.193 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:L.49, C:F.50, C:A.53, D:I.29, D:Y.61, D:Y.63, D:Y.63, D:I.93 Hydrogen bonds: D:D.27, D:D.27 01.13: 14 residues within 4Å: Chain D: L.49, F.50, Q.52, A.53, H.83 Chain E: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 12 PLIP interactions: 8 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:L.24, E:I.29, E:Y.61, E:Y.63, E:Y.63, E:I.93, D:L.49, D:L.49, D:L.49, D:F.50 Hydrogen bonds: E:D.27, E:D.27 01.16: 14 residues within 4Å: Chain E: L.49, F.50, Q.52, A.53, H.83 Chain F: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:L.24, F:I.29, F:Y.61, F:Y.63, F:Y.63, F:I.93, E:L.49, E:F.50, E:A.53 Hydrogen bonds: F:D.27 01.19: 14 residues within 4Å: Chain F: L.49, F.50, Q.52, A.53, H.83 Chain G: R.23, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190, E.193 11 PLIP interactions: 4 interactions with chain F, 7 interactions with chain G Hydrophobic interactions: F:L.49, F:L.49, F:F.50, F:A.53, G:I.29, G:Y.61, G:Y.63, G:Y.63, G:I.91, G:I.93 Hydrogen bonds: G:D.27 01.22: 14 residues within 4Å: Chain A: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Chain G: L.49, F.50, Q.52, A.53, H.83 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain G Hydrophobic interactions: A:L.24, A:I.29, A:Y.61, A:Y.63, A:Y.63, A:I.91, A:I.93, G:L.49, G:L.49, G:F.50, G:A.53 Hydrogen bonds: A:D.27 01.25: 14 residues within 4Å: Chain H: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190, E.193 Chain N: L.49, Q.52, A.53, H.83 11 PLIP interactions: 9 interactions with chain H, 2 interactions with chain N Hydrophobic interactions: H:R.23, H:L.24, H:I.29, H:Y.61, H:Y.63, H:Y.63, H:I.93, N:L.49, N:L.49 Hydrogen bonds: H:D.27, H:D.27 01.29: 14 residues within 4Å: Chain H: L.49, F.50, Q.52, A.53, H.83 Chain I: R.23, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Ligands: MPD.28 12 PLIP interactions: 5 interactions with chain H, 7 interactions with chain I Hydrophobic interactions: H:L.49, H:L.49, H:L.49, H:F.50, H:A.53, I:D.27, I:I.29, I:I.29, I:Y.61, I:Y.63, I:Y.63, I:I.93 01.30: 13 residues within 4Å: Chain I: L.49, F.50, Q.52, A.53, H.83 Chain J: R.23, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 12 PLIP interactions: 9 interactions with chain J, 3 interactions with chain I Hydrophobic interactions: J:D.27, J:I.29, J:I.29, J:Y.61, J:Y.63, J:Y.63, J:I.91, J:I.93, I:L.49, I:L.49, I:F.50 Hydrogen bonds: J:D.27 01.33: 14 residues within 4Å: Chain J: L.49, F.50, Q.52, A.53, H.83 Chain K: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 12 PLIP interactions: 9 interactions with chain K, 3 interactions with chain J Hydrophobic interactions: K:L.24, K:D.27, K:I.29, K:I.29, K:Y.61, K:Y.63, K:Y.63, K:I.93, J:L.49, J:L.49, J:F.50 Hydrogen bonds: K:D.27 01.36: 12 residues within 4Å: Chain K: L.49, F.50, Q.52, A.53 Chain L: R.23, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 10 PLIP interactions: 3 interactions with chain K, 7 interactions with chain L Hydrophobic interactions: K:L.49, K:L.49, K:F.50, L:D.27, L:I.29, L:Y.61, L:Y.63, L:Y.63, L:I.93 Hydrogen bonds: L:D.27 01.41: 13 residues within 4Å: Chain L: L.49, F.50, Q.52, A.53, H.83 Chain M: R.23, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 11 PLIP interactions: 9 interactions with chain M, 2 interactions with chain L Hydrophobic interactions: M:D.27, M:I.29, M:Y.61, M:Y.63, M:Y.63, M:I.91, M:I.93, L:L.49, L:F.50 Hydrogen bonds: M:D.27, M:D.27 01.44: 13 residues within 4Å: Chain M: L.49, F.50, Q.52, A.53, H.83 Chain N: R.23, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 11 PLIP interactions: 7 interactions with chain N, 4 interactions with chain M Hydrophobic interactions: N:I.29, N:Y.61, N:Y.63, N:Y.63, N:I.93, M:L.49, M:L.49, M:F.50, M:A.53 Hydrogen bonds: N:D.27, N:D.27

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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