SMTL ID : 6exm.1

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (MK202)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x QQH: [(3~{R})-3-carboxy-7-[(2,3-dimethylphenyl)methyl]-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridin-8-yl]-dimethyl-azanium(Non-covalent)

QQH.1: 13 residues within 4Å: Chain A: Q.63, Y.64, Y.65, K.66, F.69, K.124, Y.128, Q.148, I.151, V.155, W.226, F.227, C.231 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.64, A:K.66, A:I.151 Water bridges: A:K.66, A:K.66, A:K.66 Salt bridges: A:K.66 pi-Stacking: A:W.226 QQH.8: 13 residues within 4Å: Chain B: Q.63, Y.64, Y.65, K.66, F.69, K.124, Y.128, I.151, L.152, V.155, W.226, F.227, C.231 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.64, B:K.66, B:I.151, B:L.152 Water bridges: B:K.66 Salt bridges: B:K.124 pi-Stacking: B:W.226

3 x NA: SODIUM ION(Non-functional Binders)

NA.2: 2 residues within 4Å: Chain A: N.32, E.38 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.38, A:S.73 NA.3: 2 residues within 4Å: Chain A: G.236, N.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.236 NA.9: 3 residues within 4Å: Chain B: N.32, D.35, E.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.32

4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 7 residues within 4Å: Chain A: L.50, Y.65, I.71, M.72, Q.125 Chain B: V.126, L.130 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.50, A:I.71, B:V.126, B:L.130 Hydrogen bonds: A:Q.125, A:Q.125 Water bridges: A:M.72 IPA.5: 6 residues within 4Å: Chain A: M.173, Q.174, G.177, K.196, I.201, F.208 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.201, A:F.208 Hydrogen bonds: A:K.196 IPA.6: 7 residues within 4Å: Chain A: V.126, L.130 Chain B: L.50, Y.65, I.71, M.72, Q.125 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.126, A:L.130, B:L.50, B:I.71 Hydrogen bonds: B:Y.65, B:Q.125, B:Q.125 Water bridges: B:M.72 IPA.7: 6 residues within 4Å: Chain A: L.29, T.51, I.53, I.59, N.86, E.88 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.53, A:I.59 Hydrogen bonds: A:T.51, A:T.51, A:E.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kulen, M. et al., Structure-Based Design of Inhibitors Targeting PrfA, the Master Virulence Regulator of Listeria monocytogenes. J. Med. Chem. (2018)

Release Date

2018-05-02

Peptides

Listeriolysin positive regulatory factor A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Listeriolysin positive regulatory factor A

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