SMTL ID : 8szn.1 (1 other biounit)

Crystal structure of Neisseria meningitidis ClpP protease in complex with phosphine oxide compound ACP6-12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-14-mer

Ligands

12 x X3O: 2-{bis[5-(trifluoromethyl)pyridin-2-yl]phosphoryl}-2-methyl-N-(2-{[2-(trifluoromethyl)phenyl]sulfanyl}ethyl)propanamide(Non-covalent)

X3O.1: 16 residues within 4Å: Chain A: R.27, L.28, E.31, I.33, F.65, Y.67, F.117, L.119, R.199, L.202 Chain G: L.53, F.54, S.57, T.84, F.87, I.88 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain G Hydrophobic interactions: A:E.31, A:F.65, A:F.65, A:Y.67 Hydrogen bonds: A:Y.67, A:R.199, A:R.199 Halogen bonds: A:R.27 pi-Stacking: G:F.87 X3O.2: 16 residues within 4Å: Chain A: L.53, F.54, S.57, T.84, F.87 Chain B: R.27, L.28, E.31, I.33, F.65, Y.67, L.95, F.117, L.119, L.196, R.199 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:E.31, B:I.33, B:F.65, B:F.65, B:L.95 Hydrogen bonds: B:Y.67, B:R.199, B:R.199 pi-Stacking: A:F.87 Halogen bonds: A:T.84 X3O.3: 16 residues within 4Å: Chain B: L.53, F.54, S.57, T.84, F.87, I.88 Chain C: R.27, L.28, E.31, I.33, F.65, Y.67, F.117, L.119, L.196, R.199 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:E.31, C:F.65, C:L.196 Hydrogen bonds: C:Y.67, C:R.199, C:R.199 Halogen bonds: C:R.27, B:L.53 pi-Stacking: B:F.87 X3O.4: 16 residues within 4Å: Chain D: L.53, S.57, E.58, T.84, F.87, I.88 Chain E: R.27, L.28, E.31, I.33, F.65, Y.67, L.95, F.117, L.119, R.199 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:E.31, E:F.65, E:F.65, E:Y.67, E:L.95, D:L.53 Hydrogen bonds: E:Y.67, E:R.199, E:R.199 Halogen bonds: E:R.27 pi-Stacking: D:F.87 X3O.5: 18 residues within 4Å: Chain E: L.53, F.54, S.57, T.84, F.87, I.88 Chain F: R.27, L.28, E.31, I.33, F.65, Y.67, L.95, F.117, L.119, L.196, R.199, L.202 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:E.31, F:F.65, F:F.65, F:L.95, F:L.196 Hydrogen bonds: F:Y.67, F:R.199, F:R.199 Halogen bonds: F:R.27 pi-Stacking: E:F.87 X3O.6: 17 residues within 4Å: Chain F: L.53, F.54, S.57, T.84, F.87, I.88 Chain G: R.27, L.28, E.31, I.33, F.65, Y.67, L.95, F.117, L.119, L.196, R.199 12 PLIP interactions: 9 interactions with chain G, 3 interactions with chain F Hydrophobic interactions: G:E.31, G:F.65, G:F.65, G:Y.67, G:L.95, G:L.196 Hydrogen bonds: G:Y.67, G:R.199, G:R.199 pi-Stacking: F:F.87 Halogen bonds: F:L.53, F:T.84 X3O.7: 16 residues within 4Å: Chain H: R.27, L.28, E.31, I.33, F.65, Y.67, F.117, L.119, R.199, L.202 Chain N: L.53, F.54, S.57, T.84, F.87, I.88 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain N Hydrophobic interactions: H:E.31, H:F.65, H:F.65, H:Y.67 Hydrogen bonds: H:Y.67, H:R.199, H:R.199 Halogen bonds: H:R.27 pi-Stacking: N:F.87 X3O.8: 16 residues within 4Å: Chain H: L.53, F.54, S.57, T.84, F.87 Chain I: R.27, L.28, E.31, I.33, F.65, Y.67, L.95, F.117, L.119, L.196, R.199 10 PLIP interactions: 8 interactions with chain I, 2 interactions with chain H Hydrophobic interactions: I:E.31, I:I.33, I:F.65, I:F.65, I:L.95 Hydrogen bonds: I:Y.67, I:R.199, I:R.199 pi-Stacking: H:F.87 Halogen bonds: H:T.84 X3O.9: 16 residues within 4Å: Chain I: L.53, F.54, S.57, T.84, F.87, I.88 Chain J: R.27, L.28, E.31, I.33, F.65, Y.67, F.117, L.119, L.196, R.199 9 PLIP interactions: 7 interactions with chain J, 2 interactions with chain I Hydrophobic interactions: J:E.31, J:F.65, J:L.196 Hydrogen bonds: J:Y.67, J:R.199, J:R.199 Halogen bonds: J:R.27, I:L.53 pi-Stacking: I:F.87 X3O.10: 16 residues within 4Å: Chain K: L.53, S.57, E.58, T.84, F.87, I.88 Chain L: R.27, L.28, E.31, I.33, F.65, Y.67, L.95, F.117, L.119, R.199 11 PLIP interactions: 9 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:E.31, L:F.65, L:F.65, L:Y.67, L:L.95, K:L.53 Hydrogen bonds: L:Y.67, L:R.199, L:R.199 Halogen bonds: L:R.27 pi-Stacking: K:F.87 X3O.11: 18 residues within 4Å: Chain L: L.53, F.54, S.57, T.84, F.87, I.88 Chain M: R.27, L.28, E.31, I.33, F.65, Y.67, L.95, F.117, L.119, L.196, R.199, L.202 10 PLIP interactions: 1 interactions with chain L, 9 interactions with chain M pi-Stacking: L:F.87 Hydrophobic interactions: M:E.31, M:F.65, M:F.65, M:L.95, M:L.196 Hydrogen bonds: M:Y.67, M:R.199, M:R.199 Halogen bonds: M:R.27 X3O.12: 17 residues within 4Å: Chain M: L.53, F.54, S.57, T.84, F.87, I.88 Chain N: R.27, L.28, E.31, I.33, F.65, Y.67, L.95, F.117, L.119, L.196, R.199 12 PLIP interactions: 3 interactions with chain M, 9 interactions with chain N pi-Stacking: M:F.87 Halogen bonds: M:L.53, M:T.84 Hydrophobic interactions: N:E.31, N:F.65, N:F.65, N:Y.67, N:L.95, N:L.196 Hydrogen bonds: N:Y.67, N:R.199, N:R.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, F. et al., Structure-Based Design and Development of Phosphine Oxides as a Novel Chemotype for Antibiotics that Dysregulate Bacterial ClpP Proteases. J.Med.Chem. (2024)

Release Date

2024-09-18

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
V

B
W

C
X

D
Y

E
Z

F
a

G
b

H
V

I
W

J
X

K
Y

L
Z

M
a

N
b

ATP-dependent Clp protease proteolytic subunit

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