SMTL ID : 4nat.1

Inhibitors of 4-Phosphopanthetheine Adenylyltransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-hexamer

Ligands

6 x 2W5: (1R,2R)-N-(3,4-dichlorobenzyl)-2-(4,6-dimethoxypyrimidin-2-yl)cyclohexanecarboxamide(Non-covalent)

2W5.1: 15 residues within 4Å: Chain A: P.9, G.10, C.36, L.38, F.71, G.73, L.74, L.75, R.89, L.103, M.106, N.107 Chain B: E.135, V.136, Y.139 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.74, A:L.103, B:V.136 Hydrogen bonds: A:L.75, B:E.135 Water bridges: A:V.76, B:E.135 Halogen bonds: A:C.36 2W5.4: 15 residues within 4Å: Chain B: P.9, G.10, C.36, L.38, F.71, G.73, L.74, L.75, R.89, L.103, M.106, N.107 Chain C: E.135, V.136, Y.139 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.38, B:L.74, B:L.103, B:M.106, C:V.136 Hydrogen bonds: B:L.75, C:E.135 Water bridges: B:V.76 Halogen bonds: B:C.36, B:C.36 2W5.7: 17 residues within 4Å: Chain A: E.135, V.136, Y.139 Chain C: P.9, G.10, C.36, V.37, L.38, F.71, G.73, L.74, L.75, R.89, L.103, M.106, N.107 Ligands: ADP.8 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.38, C:L.74, C:L.75, C:L.103, C:M.106, A:V.136 Hydrogen bonds: C:L.75, A:E.135 Water bridges: C:N.107 Halogen bonds: C:C.36 2W5.9: 15 residues within 4Å: Chain D: P.9, G.10, C.36, L.38, F.71, G.73, L.74, L.75, R.89, L.103, M.106, N.107 Chain E: E.135, V.136, Y.139 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:L.74, D:L.103, E:V.136 Hydrogen bonds: D:L.75, E:E.135 Water bridges: D:V.76 Halogen bonds: D:C.36 2W5.12: 15 residues within 4Å: Chain E: P.9, G.10, C.36, L.38, F.71, G.73, L.74, L.75, R.89, L.103, M.106, N.107 Chain F: E.135, V.136, Y.139 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:L.38, E:L.74, E:L.103, E:M.106, F:V.136 Hydrogen bonds: E:L.75, F:E.135 Water bridges: E:V.76 Halogen bonds: E:C.36, E:C.36 2W5.15: 17 residues within 4Å: Chain D: E.135, V.136, Y.139 Chain F: P.9, G.10, C.36, V.37, L.38, F.71, G.73, L.74, L.75, R.89, L.103, M.106, N.107 Ligands: ADP.16 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain D Hydrophobic interactions: F:L.38, F:L.74, F:L.75, F:L.103, F:M.106, D:V.136 Hydrogen bonds: F:L.75, D:E.135 Water bridges: F:N.107 Halogen bonds: F:C.36

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 6 residues within 4Å: Chain A: L.74, D.77, L.110 Chain B: Y.139, R.140, A.141 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.77, A:D.77 EPE.5: 1 residues within 4Å: Chain B: P.149 No protein-ligand interaction detected (PLIP) EPE.10: 6 residues within 4Å: Chain D: L.74, D.77, L.110 Chain E: Y.139, R.140, A.141 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:D.77, D:D.77 EPE.13: 1 residues within 4Å: Chain E: P.149 No protein-ligand interaction detected (PLIP)

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 7 residues within 4Å: Chain A: P.9, G.10, S.11, F.12, H.19, R.89, Y.99 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:P.9, A:S.11, A:F.12 Water bridges: A:S.130 Salt bridges: A:H.19, A:R.89 pi-Stacking: A:Y.99, A:Y.99 ADP.6: 6 residues within 4Å: Chain B: G.10, S.11, F.12, H.19, R.89, Y.99 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.11, B:F.12, B:R.89, B:R.89 Salt bridges: B:H.19 pi-Stacking: B:Y.99, B:Y.99 ADP.8: 10 residues within 4Å: Chain C: G.10, S.11, F.12, H.19, R.89, R.92, S.95, D.96, Y.99 Ligands: 2W5.7 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.11, C:F.12, C:D.13, C:R.92, C:R.92, C:D.96, C:E.100 Water bridges: C:H.19, C:Y.99, C:S.130, C:S.130 Salt bridges: C:H.19, C:R.89 pi-Stacking: C:Y.99, C:Y.99 ADP.11: 7 residues within 4Å: Chain D: P.9, G.10, S.11, F.12, H.19, R.89, Y.99 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:P.9, D:S.11, D:F.12 Water bridges: D:S.130 Salt bridges: D:H.19, D:R.89 pi-Stacking: D:Y.99, D:Y.99 ADP.14: 6 residues within 4Å: Chain E: G.10, S.11, F.12, H.19, R.89, Y.99 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.11, E:F.12, E:R.89, E:R.89 Salt bridges: E:H.19 pi-Stacking: E:Y.99, E:Y.99 ADP.16: 10 residues within 4Å: Chain F: G.10, S.11, F.12, H.19, R.89, R.92, S.95, D.96, Y.99 Ligands: 2W5.15 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:S.11, F:F.12, F:D.13, F:R.92, F:R.92, F:E.100, F:E.100 Water bridges: F:H.19, F:Y.99, F:S.130, F:S.130 Salt bridges: F:H.19, F:R.89 pi-Stacking: F:Y.99, F:Y.99

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
A

E
B

F
C

Phosphopantetheine adenylyltransferase

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