SMTL ID : 6l3x.1

Discovery of novel peptidomimetic boronate ClpP inhibitors with noncanonical enzyme mechanism as potent virulence blockers in vitro and in vivo

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-14-mer

Ligands

14 x E4U: [(1~{R})-1-[[(2~{S})-2-[[2,5-bis(chloranyl)phenyl]carbonylamino]-3-(1~{H}-indol-3-yl)propanoyl]amino]-3-methyl-butyl]boronic acid(Non-covalent)(Covalent)

E4U.1: 13 residues within 4Å: Chain A: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, G.110, I.125 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.53, A:P.107 Hydrogen bonds: A:G.51, A:G.51, A:G.51, A:S.80, A:M.81, A:H.105, A:L.108 E4U.2: 12 residues within 4Å: Chain B: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, I.125 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.51, B:G.51, B:G.51, B:M.81, B:L.108 E4U.3: 13 residues within 4Å: Chain C: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, G.110, I.125 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.53, C:P.107 Hydrogen bonds: C:G.51, C:G.51, C:G.51, C:M.81, C:L.108 E4U.4: 13 residues within 4Å: Chain D: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, G.110, I.125 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.53 Hydrogen bonds: D:G.51, D:G.51, D:G.51, D:S.80, D:M.81, D:L.108 E4U.5: 12 residues within 4Å: Chain E: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, I.125 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:V.53, E:P.107 Hydrogen bonds: E:G.51, E:G.51, E:G.51, E:M.81, E:L.108 E4U.6: 12 residues within 4Å: Chain F: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, I.125 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:V.53, F:P.107 Hydrogen bonds: F:G.51, F:G.51, F:S.80, F:M.81, F:H.105, F:L.108 E4U.7: 13 residues within 4Å: Chain G: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, G.110, I.125 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:V.53, G:P.107 Hydrogen bonds: G:G.51, G:G.51, G:G.51, G:S.80, G:M.81, G:H.105, G:L.108 E4U.8: 13 residues within 4Å: Chain H: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, G.110, I.125 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:V.53, H:P.107, H:I.125 Hydrogen bonds: H:G.51, H:G.51, H:G.51, H:S.80, H:M.81, H:H.105, H:L.108 E4U.9: 13 residues within 4Å: Chain I: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, G.110, I.125 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:V.53, I:P.107 Hydrogen bonds: I:G.51, I:G.51, I:S.80, I:M.81, I:H.105, I:L.108 E4U.10: 13 residues within 4Å: Chain J: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, I.125, L.132 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:L.132 Hydrogen bonds: J:G.51, J:G.51, J:S.80, J:M.81, J:H.105, J:L.108 E4U.11: 13 residues within 4Å: Chain K: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, G.110, I.125 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:V.53, K:P.107 Hydrogen bonds: K:G.51, K:G.51, K:G.51, K:S.80, K:M.81, K:L.108 E4U.12: 13 residues within 4Å: Chain L: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, G.110, I.125 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:V.53, L:P.107 Hydrogen bonds: L:G.51, L:G.51, L:G.51, L:M.81, L:L.108 E4U.13: 13 residues within 4Å: Chain M: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, G.110, I.125 7 PLIP interactions: 7 interactions with chain M Hydrophobic interactions: M:V.53 Hydrogen bonds: M:G.51, M:G.51, M:G.51, M:S.80, M:M.81, M:L.108 E4U.14: 12 residues within 4Å: Chain N: G.50, G.51, S.52, V.53, S.80, M.81, H.105, Q.106, P.107, L.108, G.109, G.110 9 PLIP interactions: 9 interactions with chain N Hydrophobic interactions: N:V.53, N:P.107 Hydrogen bonds: N:G.51, N:G.51, N:G.51, N:S.80, N:M.81, N:H.105, N:L.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ju, Y. et al., Discovery of Novel Peptidomimetic Boronate ClpP Inhibitors with Noncanonical Enzyme Mechanism as Potent Virulence Blockersin Vitroandin Vivo. J.Med.Chem. (2020)

Release Date

2020-08-26

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