SMTL ID : 7ss7.1

Crystal structure of Klebsiella LpxH in complex with JH-LPH-50

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.8, H.10, D.41, H.197 Ligands: MN.2, BN8.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.8, A:H.10, A:D.41, A:H.197 MN.2: 7 residues within 4Å: Chain A: D.8, D.41, N.79, H.114, H.195 Ligands: MN.1, BN8.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.41, A:H.114, A:H.195

1 x BN8: 6-{[(4-{4-[3-chloro-5-(trifluoromethyl)phenyl]piperazine-1-sulfonyl}phenyl)carbamoyl]amino}-N-hydroxyhexanamide(Non-covalent)

BN8.3: 23 residues within 4Å: Chain A: D.8, H.10, D.41, A.45, W.46, N.79, R.80, F.82, L.83, H.114, Y.125, V.132, Q.138, F.141, I.152, A.153, M.156, M.172, H.195, H.197 Ligands: MN.1, MN.2, EDO.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.82, A:F.141 Hydrogen bonds: A:W.46, A:N.79, A:R.80 Water bridges: A:R.80 pi-Stacking: A:F.141 pi-Cation interactions: A:R.80

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: E.15, I.18, H.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.220 EDO.5: 7 residues within 4Å: Chain A: D.49, D.50, D.51, P.52, Q.57, R.87, Q.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.49, A:Q.57, A:Q.91 Water bridges: A:P.52 EDO.6: 4 residues within 4Å: Chain A: D.51, N.53, H.56, H.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.53, A:H.56 Water bridges: A:H.150 EDO.7: 3 residues within 4Å: Chain A: A.89, G.93, M.94 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.64, A:K.64, A:K.64, A:Q.86, A:G.93 EDO.8: 3 residues within 4Å: Chain A: D.104, L.105, Y.106 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.106 EDO.9: 1 residues within 4Å: Ligands: BN8.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwak, S.H. et al., Development of LpxH Inhibitors Chelating the Active Site Dimanganese Metal Cluster of LpxH. Chemmedchem (2023)

Release Date

2023-04-12

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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