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SMTL ID : 9f8l.2 (1 other biounit)

Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with [6-Hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl](3-hydroxyphenyl)methanone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1:	12 residues within 4Å: Chain A: R.58, R.61, L.73, H.93, S.97, F.101, W.104, W.106, Y.140, F.144, E.160 Ligands: 01.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.97 Water bridges: A:E.160 Salt bridges: A:R.58, A:R.61, A:E.160 pi-Cation interactions: A:F.101
MES.6:	12 residues within 4Å: Chain B: R.58, R.61, L.73, H.93, S.97, F.101, W.104, W.106, Y.140, F.144, E.160 Ligands: 01.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.97 Water bridges: B:E.160, B:E.160 Salt bridges: B:R.58, B:R.61, B:E.160 pi-Cation interactions: B:F.101

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2:	5 residues within 4Å: Chain A: R.44, E.48, H.52, I.109, I.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.52 Water bridges: A:R.44, A:I.109
GOL.4:	6 residues within 4Å: Chain A: Q.115, D.116, W.119 Chain B: Q.110, I.111, F.112 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.111, A:Q.115 Water bridges: B:R.44, B:I.109, A:D.116
GOL.5:	9 residues within 4Å: Chain A: R.40, E.113, T.114, Q.115 Chain B: R.40, E.113, T.114, Q.115 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.113, A:E.113
GOL.7:	5 residues within 4Å: Chain B: R.44, E.48, H.52, I.109, I.111 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.52 Water bridges: B:R.44, B:I.109
GOL.9:	6 residues within 4Å: Chain A: Q.110, I.111, F.112 Chain B: Q.115, D.116, W.119 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.111, B:Q.115 Water bridges: A:R.44, A:I.109, B:D.116
GOL.10:	9 residues within 4Å: Chain A: R.40, E.113, T.114, Q.115 Chain B: R.40, E.113, T.114, Q.115 Ligands: GOL.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.113, B:E.113

2 x 01: (3-hydroxyphenyl)-[2-(4-hydroxyphenyl)-6-oxidanyl-1-benzothiophen-3-yl]methanone

01.3:

20 residues within 4Å:

Chain A: G.72, L.73, T.76, D.77, I.82, I.84, H.93, W.96, S.97, F.101, F.132, M.162, P.164, Q.167, F.168
Chain B: V.178, R.180, L.183, P.184
Ligands: MES.1

11 PLIP interactions:

3 interactions with chain B, 8 interactions with chain A

Hydrophobic interactions: B:V.178, B:L.183, A:L.73, A:L.73, A:I.82, A:W.96
Hydrogen bonds: B:P.184, A:D.77, A:H.93, A:Q.167
pi-Stacking: A:F.132

01.8:

20 residues within 4Å:

Chain A: V.178, R.180, L.183, P.184
Chain B: G.72, L.73, T.76, D.77, I.82, I.84, H.93, W.96, S.97, F.101, F.132, M.162, P.164, Q.167, F.168
Ligands: MES.6

12 PLIP interactions:

9 interactions with chain B, 3 interactions with chain A

Hydrophobic interactions: B:L.73, B:L.73, B:I.82, B:W.96, A:V.178, A:L.183
Hydrogen bonds: B:D.77, B:D.77, B:H.93, B:Q.167, A:P.184
pi-Stacking: B:F.132

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Thiemann, M. et al., From Bones to Bugs: Structure-Based Development of Raloxifene-Derived Pathoblockers That Inhibit Pyocyanin Production in Pseudomonas aeruginosa. J.Med.Chem. (2025)

Release Date