SMTL ID : 8szn.2 (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

5 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 H: R.27, L.28, E.31, I.33, F.65, Y.67, L.95, F.117, L.119, R.199 Chain N: L.53, F.54, S.57, T.84, F.87, I.88 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain N Hydrophobic interactions: H:E.31, H:F.65, H:F.65, H:Y.67, H:L.95 Hydrogen bonds: H:Y.67, H:R.199, H:R.199 pi-Stacking: H:Y.67, N:F.87 Halogen bonds: H:R.27 X3O.2: 15 residues within 4Å: Chain I: L.53, F.54, S.57, D.83, T.84, F.87 Chain J: R.27, L.28, E.31, I.33, F.65, Y.67, F.117, L.119, R.199 9 PLIP interactions: 8 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:I.33, J:F.65, J:F.65, J:F.65 Hydrogen bonds: J:Y.67, J:R.199, J:R.199 Halogen bonds: J:R.27 pi-Stacking: I:F.87 X3O.3: 15 residues within 4Å: Chain K: L.53, F.54, S.57, T.84, F.87 Chain L: R.27, L.28, E.31, I.33, F.65, Y.67, L.95, F.117, L.119, L.196 7 PLIP interactions: 2 interactions with chain K, 5 interactions with chain L Hydrophobic interactions: K:F.87, L:E.31, L:F.65, L:F.65, L:L.95 Halogen bonds: K:L.53 Hydrogen bonds: L:Y.67 X3O.4: 15 residues within 4Å: Chain L: L.53, F.54, S.57, T.84, F.87 Chain M: R.27, L.28, E.31, F.65, Y.67, L.95, F.117, L.119, L.196, R.199 12 PLIP interactions: 9 interactions with chain M, 3 interactions with chain L 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, L:L.53, L:T.84 pi-Stacking: L:F.87 X3O.5: 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 14 PLIP interactions: 4 interactions with chain M, 10 interactions with chain N Hydrophobic interactions: M:F.87, M:F.87, N:E.31, N:I.33, N:F.65, N:Y.67, N:L.95, N:L.196 Halogen bonds: M:F.54, M:T.84, N:R.27 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
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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