SMTL ID : 9k2c.1

Structure of ClpP from Staphylococcus aureus in complex with ZY1

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-(1~{H}-imidazol-5-ylmethyl)-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: 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: V.45, L.49, F.50, A.53, H.83 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain G Hydrophobic interactions: A:L.24, A:D.27, A:I.29, A:I.29, A:Y.61, A:Y.63, A:Y.63, A:I.93, G:V.45, G:L.49, G:L.49, G:L.49, G:F.50, G:A.53 Hydrogen bonds: A:D.27, A:D.27 Water bridges: G:Q.52 01.4: 15 residues within 4Å: Chain A: L.49, F.50, Q.52, A.53, H.83 Chain B: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 Ligands: MPD.6 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:L.49, A:L.49, A:L.49, A:A.53, B:L.24, B:D.27, B:I.29, B:I.29, B:Y.61, B:Y.63, B:I.93 Hydrogen bonds: B:D.27, B:D.27 01.8: 15 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, M.31, Y.61, Y.63, I.91, I.93, M.190 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.24, C:D.27, C:I.29, C:I.29, C:Y.61, C:Y.63, C:I.91, C:I.93, B:L.49, B:L.49, B:A.53 Hydrogen bonds: C:D.27 01.11: 13 residues within 4Å: Chain C: L.49, Q.52, A.53, H.83 Chain D: R.23, L.24, D.27, I.29, M.31, Y.61, Y.63, I.91, M.190 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:L.49, C:L.49, C:A.53, D:L.24, D:I.29, D:I.29, D:Y.61, D:Y.63, D:Y.63 Hydrogen bonds: D:D.27 01.14: 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 11 PLIP interactions: 7 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:L.24, E:I.29, E:I.29, E:Y.61, E:Y.63, E:I.93, D:L.49, D:L.49, D:L.49, D:A.53 Hydrogen bonds: E:D.27 01.17: 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 14 PLIP interactions: 3 interactions with chain E, 11 interactions with chain F Hydrophobic interactions: E:L.49, E:L.49, E:A.53, F:L.24, F:D.27, F:I.29, F:I.29, F:Y.61, F:Y.63, F:Y.63, F:I.91, F:I.93 Hydrogen bonds: F:D.27, F:D.27 01.20: 14 residues within 4Å: Chain F: L.49, F.50, Q.52, A.53, H.83 Chain G: R.23, L.24, D.27, I.29, 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:L.24, G:D.27, G:I.29, G:I.29, G:Y.61, G:Y.63, G:Y.63, G:I.93, F:L.49, F:A.53 Hydrogen bonds: G:D.27, G:D.27 01.23: 16 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: V.45, L.49, F.50, Q.52, A.53, H.83 13 PLIP interactions: 8 interactions with chain H, 5 interactions with chain N Hydrophobic interactions: H:L.24, H:D.27, H:I.29, H:I.29, H:Y.61, H:Y.63, H:I.93, N:V.45, N:L.49, N:L.49, N:L.49, N:A.53 Hydrogen bonds: H:D.27 01.26: 14 residues within 4Å: Chain H: L.49, F.50, Q.52, A.53, H.83 Chain I: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 16 PLIP interactions: 11 interactions with chain I, 5 interactions with chain H Hydrophobic interactions: I:L.24, I:D.27, I:I.29, I:I.29, I:Y.61, I:Y.63, I:Y.63, I:I.93, H:L.49, H:L.49, H:L.49, H:F.50, H:A.53 Water bridges: I:D.27, I:D.27, I:Y.61 01.29: 14 residues within 4Å: Chain I: L.49, F.50, Q.52, A.53, H.83 Chain J: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 18 PLIP interactions: 12 interactions with chain J, 6 interactions with chain I Hydrophobic interactions: J:L.24, J:D.27, J:I.29, J:I.29, J:Y.61, J:Y.63, J:Y.63, J:I.91, J:I.91, J:I.93, I:L.49, I:L.49, I:L.49, I:F.50, I:A.53 Hydrogen bonds: J:D.27, J:D.27, I:Q.52 01.32: 16 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, M.31, Y.61, Y.63, I.91, I.93, M.190, E.193 12 PLIP interactions: 8 interactions with chain K, 4 interactions with chain J Hydrophobic interactions: K:L.24, K:I.29, K:I.29, K:Y.61, K:Y.63, K:I.93, J:L.49, J:L.49, J:L.49, J:A.53 Hydrogen bonds: K:D.27, K:D.27 01.35: 14 residues within 4Å: Chain K: L.49, F.50, Q.52, A.53, H.83 Chain L: R.23, L.24, D.27, I.29, Y.61, Y.63, I.91, I.93, M.190 12 PLIP interactions: 10 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:L.24, L:D.27, L:I.29, L:I.29, L:Y.61, L:Y.63, L:Y.63, L:I.93, K:L.49, K:A.53 Hydrogen bonds: L:D.27, L:D.27 01.38: 13 residues within 4Å: Chain L: L.49, F.50, A.53, H.83 Chain M: 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 M, 3 interactions with chain L 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, L:L.49, L:L.49, L:A.53 Hydrogen bonds: M:D.27 01.41: 14 residues within 4Å: Chain M: L.49, Q.52, 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 14 PLIP interactions: 11 interactions with chain N, 3 interactions with chain M Hydrophobic interactions: N:L.24, N:L.24, N:D.27, N:I.29, N:I.29, N:Y.61, N:Y.63, N:Y.63, N:I.93, M:L.49, M:L.49, M:A.53 Hydrogen bonds: N:D.27 Water bridges: N:Y.61

14 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:I.81, A:P.86, H2O.3, H2O.4 MG.5: 3 residues within 4Å: Chain B: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:I.81, B:P.86, H2O.5, H2O.8 MG.9: 3 residues within 4Å: Chain C: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:I.81, C:P.86, H2O.10, H2O.11 MG.12: 3 residues within 4Å: Chain D: I.81, I.84, P.86 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:I.81, D:P.86, H2O.13 MG.15: 4 residues within 4Å: Chain E: I.81, I.84, P.86, V.88 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:I.81, E:P.86, H2O.16 MG.18: 4 residues within 4Å: Chain F: I.81, I.84, P.86, V.88 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:I.81, F:P.86, H2O.18 MG.21: 3 residues within 4Å: Chain G: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:I.81, G:P.86, H2O.20, H2O.21 MG.24: 3 residues within 4Å: Chain H: I.81, I.84, P.86 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:I.81, H:P.86, H2O.22, H2O.24 MG.27: 3 residues within 4Å: Chain I: I.81, I.84, P.86 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:I.81, I:P.86, H2O.27 MG.30: 3 residues within 4Å: Chain J: I.81, I.84, P.86 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:I.81, J:P.86, H2O.30 MG.33: 3 residues within 4Å: Chain K: I.81, I.84, P.86 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:I.81, K:P.86, H2O.33 MG.36: 4 residues within 4Å: Chain L: I.81, I.84, P.86, V.88 3 PLIP interactions: 2 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:I.81, L:P.86, H2O.35 MG.39: 3 residues within 4Å: Chain M: I.81, I.84, P.86 3 PLIP interactions: 2 interactions with chain M, 1 Ligand-Water interactions Metal complexes: M:I.81, M:P.86, H2O.37 MG.42: 3 residues within 4Å: Chain N: I.81, I.84, P.86 3 PLIP interactions: 2 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:I.81, N:P.86, H2O.39

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

MPD.3: 9 residues within 4Å: Chain A: 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 A Hydrophobic interactions: A:V.71, A:F.102, A:L.150 Hydrogen bonds: A:H.123, A:H.123 Water bridges: A:S.98 MPD.6: 5 residues within 4Å: Chain A: F.50, A.53, Q.54 Chain B: R.23 Ligands: 01.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.50, A:A.53 Hydrogen bonds: B:R.23 MPD.7: 9 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:V.71, B:F.102, B:L.150 Hydrogen bonds: B:H.123, B:H.123 MPD.10: 9 residues within 4Å: Chain C: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.71, C:F.102, C:L.150, C:L.154 Hydrogen bonds: C:S.101, C:H.123, C:H.123 MPD.13: 8 residues within 4Å: Chain D: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.102, D:L.150 Hydrogen bonds: D:H.123, D:H.123 MPD.16: 10 residues within 4Å: Chain E: V.71, 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 E Hydrophobic interactions: E:V.71, E:F.102, E:L.150 Hydrogen bonds: E:H.123, E:H.123 MPD.19: 10 residues within 4Å: Chain F: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150, L.154 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:I.122, F:P.125, F:L.150 Hydrogen bonds: F:H.123 Water bridges: F:S.98, F:M.99 MPD.22: 10 residues within 4Å: Chain G: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:V.71, G:L.150, G:T.169 Hydrogen bonds: G:H.123, G:H.123 MPD.25: 9 residues within 4Å: Chain H: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:V.71, H:F.102, H:L.150, H:L.154 Hydrogen bonds: H:S.101, H:H.123, H:H.123 MPD.28: 9 residues within 4Å: Chain I: 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 I Hydrophobic interactions: I:V.71, I:F.102, I:L.150 Hydrogen bonds: I:H.123, I:H.123 MPD.31: 8 residues within 4Å: Chain J: V.71, S.98, M.99, S.101, I.122, H.123, L.150, L.154 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:V.71, J:L.150, J:L.154 Hydrogen bonds: J:H.123, J:H.123 MPD.34: 9 residues within 4Å: Chain K: 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 K Hydrophobic interactions: K:V.71, K:F.102, K:L.150 Hydrogen bonds: K:H.123, K:H.123 MPD.37: 9 residues within 4Å: Chain L: 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 L Hydrophobic interactions: L:V.71, L:F.102, L:L.150 Hydrogen bonds: L:H.123, L:H.123 MPD.40: 9 residues within 4Å: Chain M: 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 M Hydrophobic interactions: M:V.71, M:F.102, M:L.150 Hydrogen bonds: M:H.123, M:H.123 MPD.43: 9 residues within 4Å: Chain N: 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 N Hydrophobic interactions: N:V.71, N:F.102, N:L.150, N:L.154 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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