SMTL ID : 4nah.1

Inhibitors of 4-Phosphopanthetheine Adenylyltransferase (PPAT)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-hexamer

Ligands

6 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 18 residues within 4Å: Chain A: P.9, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, D.96, E.100, S.121, Y.125, I.128, S.129, S.130, S.131 Ligands: 2VJ.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:S.11, A:S.11, A:F.12, A:H.19, A:R.89, A:G.90, A:R.92, A:S.121, A:Y.125, A:S.131, A:S.131, A:S.131, A:S.131 Water bridges: A:R.92, A:R.92 Salt bridges: A:H.19, A:R.92 pi-Cation interactions: A:R.92 AGS.4: 18 residues within 4Å: Chain B: P.9, G.10, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, D.96, E.100, S.121, Y.125, I.128, S.129, S.130, S.131 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:S.11, B:S.11, B:F.12, B:R.89, B:G.90, B:R.92, B:R.92, B:S.121, B:Y.125, B:S.129, B:S.130, B:S.131 Water bridges: B:H.19, B:H.19, B:I.128, B:S.130 Salt bridges: B:H.19 pi-Cation interactions: B:R.92 AGS.6: 18 residues within 4Å: Chain C: P.9, G.10, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, D.96, E.100, S.121, Y.125, I.128, S.129, S.130, S.131 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:S.11, C:S.11, C:F.12, C:R.89, C:G.90, C:R.92, C:R.92, C:S.121, C:Y.125, C:S.129, C:S.130, C:S.131 Water bridges: C:H.19, C:R.89, C:I.128 Salt bridges: C:H.19 pi-Cation interactions: C:R.92 AGS.7: 18 residues within 4Å: Chain D: P.9, G.10, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, D.96, E.100, S.121, Y.125, I.128, S.129, S.130, S.131 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:S.11, D:F.12, D:R.89, D:G.90, D:R.92, D:R.92, D:E.100, D:E.100, D:S.121, D:I.128, D:S.130, D:S.131 Water bridges: D:T.16, D:S.130 Salt bridges: D:H.19, D:R.92 pi-Cation interactions: D:R.92 AGS.9: 18 residues within 4Å: Chain E: P.9, G.10, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, D.96, E.100, S.121, Y.125, I.128, S.129, S.130, S.131 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:S.11, E:S.11, E:F.12, E:H.19, E:R.89, E:G.90, E:R.92, E:R.92, E:Y.125, E:S.130 Water bridges: E:H.19, E:R.89, E:I.128 Salt bridges: E:H.19 pi-Cation interactions: E:R.92 AGS.10: 17 residues within 4Å: Chain F: G.10, S.11, F.12, G.18, H.19, I.22, R.89, G.90, R.92, D.96, E.100, S.121, Y.125, I.128, S.129, S.130, S.131 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:S.11, F:S.11, F:F.12, F:H.19, F:R.89, F:G.90, F:R.92, F:S.121, F:I.128, F:S.130, F:S.130, F:S.131 Salt bridges: F:H.19, F:H.19, F:R.92

6 x 2VJ: 2-[(2-{(1S,2S)-2-[(3,4-dichlorobenzyl)carbamoyl]cyclohexyl}-6-ethylpyrimidin-4-yl)sulfanyl]-1H-imidazole-5-carboxylic acid(Non-covalent)

2VJ.2: 17 residues within 4Å: Chain A: I.132, E.135, V.136, Y.139 Chain C: P.9, C.36, V.37, L.38, K.43, G.73, L.74, L.75, R.89, Y.99, E.100, M.106, N.107 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:P.9, C:L.74, C:L.75, C:L.75, C:R.89, A:I.132, A:V.136 Hydrogen bonds: C:L.75, C:N.107, A:E.135 Halogen bonds: C:C.36 2VJ.3: 18 residues within 4Å: Chain A: P.9, G.10, S.11, C.36, V.37, L.38, F.71, G.73, L.74, L.75, R.89, Y.99, L.103, M.106, N.107 Chain B: E.135, Y.139 Ligands: AGS.1 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.9, A:L.74, A:L.75, A:L.103, A:M.106 Hydrogen bonds: A:S.11, A:L.75, A:R.89, A:Y.99, A:N.107, B:E.135 Halogen bonds: A:C.36 2VJ.5: 18 residues within 4Å: Chain B: P.9, G.10, C.36, V.37, L.38, F.71, G.73, L.74, L.75, R.89, Y.99, E.100, L.103, M.106, N.107 Chain C: E.135, V.136, Y.139 14 PLIP interactions: 3 interactions with chain C, 11 interactions with chain B Hydrophobic interactions: C:V.136, B:P.9, B:L.38, B:L.74, B:L.75, B:L.103 Hydrogen bonds: C:E.135, C:E.135, B:L.75, B:Y.99, B:Y.99 Water bridges: B:N.107 Halogen bonds: B:C.36, B:C.36 2VJ.8: 18 residues within 4Å: Chain D: P.9, G.10, C.36, V.37, L.38, G.73, L.74, L.75, R.89, Y.99, E.100, L.103, M.106, N.107, L.110 Chain E: E.135, V.136, Y.139 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:L.74, D:L.75, D:L.75, D:L.75, D:L.103, D:L.103, D:M.106, D:L.110, E:V.136 Hydrogen bonds: D:L.75, D:Y.99, D:Y.99, D:N.107, E:E.135, E:E.135 Halogen bonds: D:C.36 2VJ.11: 16 residues within 4Å: Chain E: P.9, G.10, C.36, V.37, G.73, L.74, L.75, R.89, Y.99, E.100, L.103, M.106, N.107 Chain F: E.135, V.136, Y.139 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:L.74, E:L.75, E:L.75, E:L.103, F:V.136 Hydrogen bonds: E:L.75, E:N.107, F:E.135 Halogen bonds: E:C.36 2VJ.12: 16 residues within 4Å: Chain D: E.135, V.136, Y.139 Chain F: P.9, G.10, C.36, V.37, L.38, G.73, L.74, L.75, R.89, Y.99, E.100, M.106, N.107 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:P.9, F:L.38, F:L.74, F:L.75, D:V.136 Hydrogen bonds: F:L.75, F:Y.99, F:N.107, D:Y.139 Water bridges: F:V.76 Salt bridges: F:K.43 Halogen bonds: F:C.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Jonge, B.L. et al., Discovery of inhibitors of 4'-phosphopantetheine adenylyltransferase (PPAT) to validate PPAT as a target for antibacterial therapy. Antimicrob.Agents Chemother. (2013)

Release Date

2014-03-12

Peptides

Phosphopantetheine adenylyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Phosphopantetheine adenylyltransferase

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