SMTL ID : 8szm.2 (1 other biounit)

Crystal structure of E. coli ClpP protease in complex with phosphine oxide compound ACP6-12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-14-mer

Ligands

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

X3O.1: 15 residues within 4Å: Chain C: R.36, L.37, E.40, Y.74, Y.76, I.104, F.126, L.128, L.203, R.206 Chain D: L.62, F.63, A.66, T.93, F.96 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.74, C:I.104, C:L.203, D:A.66, D:F.96 Hydrogen bonds: C:Y.76, C:R.206, C:R.206 pi-Stacking: C:Y.76 X3O.2: 16 residues within 4Å: Chain E: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, F.126, L.128, L.203, R.206 Chain F: L.62, F.63, A.66, T.93, F.96 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:E.40, E:Y.74, E:Y.76, E:I.104, E:L.203, F:A.66, F:F.96, F:F.96 Hydrogen bonds: E:Y.76, E:R.206, E:R.206 Halogen bonds: E:R.36, F:L.62

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
O

I
P

J
Q

K
R

L
S

M
T

N
U

ATP-dependent Clp protease proteolytic subunit

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