SMTL ID : 9cd0.1

Crystal structure of the Klebsiella pneumoniae LpxH / JH-LPH-106 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x 01: N-[2-(5-{4-[6-chloro-4-(trifluoromethyl)pyridin-2-yl]piperazine-1-sulfonyl}-2,3-dihydro-1H-indole-1-carbonyl)phenyl]-N-methylmethanesulfonamide

01.1: 17 residues within 4Å: Chain A: A.45, W.46, N.79, R.80, F.82, L.83, Y.125, F.128, V.132, Q.138, F.141, I.152, A.153, M.156, R.157, S.160, H.195 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.125, A:F.128, A:F.128, A:F.128, A:F.141, A:R.157 Hydrogen bonds: A:W.46, A:N.79, A:R.80, A:R.157, A:S.160 Water bridges: A:R.80 pi-Stacking: A:Y.125, A:F.141 pi-Cation interactions: A:R.80

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 3 residues within 4Å: Chain A: W.136, R.139, L.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.139, A:R.139 PEG.3: 4 residues within 4Å: Chain A: Y.37, Y.74, L.97, L.103 No protein-ligand interaction detected (PLIP)

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 5 residues within 4Å: Chain A: D.8, H.10, D.41, H.197 Ligands: MN.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, A:H.10, A:D.41, A:H.197, H2O.1 MN.5: 6 residues within 4Å: Chain A: D.8, D.41, N.79, H.114, H.195 Ligands: MN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.41, A:H.114, A:H.195, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ennis, A.F. et al., Design and Evaluation of Pyridinyl Sulfonyl Piperazine LpxH Inhibitors with Potent Antibiotic Activity Against Enterobacterales. Jacs Au (2024)

Release Date

2025-02-12

Peptides

UDP-2,3-diacylglucosamine hydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-2,3-diacylglucosamine hydrolase

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