SMTL ID : 6wii.1

Crystal structure of the K. pneumoniae LpxH/JH-LPH-41 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x U2V: 5-({[4-({4-[3-chloro-5-(trifluoromethyl)phenyl]piperazin-1-yl}sulfonyl)phenyl]carbamoyl}amino)-N-hydroxypentanamide(Non-covalent)

U2V.1: 19 residues within 4Å: Chain A: A.45, W.46, N.79, R.80, F.82, L.83, C.119, D.122, Y.125, V.132, Q.138, F.141, I.152, A.153, M.156, R.157, M.172, H.195 Ligands: DMS.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.82, A:Y.125, A:F.141 Hydrogen bonds: A:W.46, A:R.80, A:R.157, A:M.172, A:H.195 pi-Stacking: A:F.141 pi-Cation interactions: A:R.80

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

MN.2: 5 residues within 4Å: Chain A: D.8, H.10, D.41, H.197 Ligands: MN.3 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.2 MN.3: 6 residues within 4Å: Chain A: D.8, D.41, N.79, H.114, H.195 Ligands: MN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.41, A:H.114, A:H.195, H2O.2

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 2 residues within 4Å: Chain A: F.128 Ligands: U2V.1 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.128 DMS.5: 4 residues within 4Å: Chain A: R.24, E.29, M.225, F.238 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.24, A:R.24 Salt bridges: A:E.29 pi-Cation interactions: A:F.238 DMS.6: 6 residues within 4Å: Chain A: A.45, W.46, I.47, D.51, N.53, H.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.53 Salt bridges: A:D.51

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: T.3, D.34, A.35, D.104, L.105, Y.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.104, A:Y.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwak, S.H. et al., Synthesis and evaluation of sulfonyl piperazine LpxH inhibitors. Bioorg.Chem. (2020)

Release Date

2020-07-29

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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