SMTL ID : 6chn.1 (1 other biounit)

Phosphopantetheine adenylyltransferase (CoaD) in complex with methyl (R)-4-(3-(2-cyano-1-((5-methyl-7-oxo-4,7-dihydro-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino)ethyl)phenoxy)piperidine-1-carboxylate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-hexamer

Ligands

6 x F1D: methyl 4-(3-{(1R)-2-cyano-1-[(5-methyl-7-oxo-6,7-dihydro[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino]ethyl}phenoxy)piperidine-1-carboxylate(Non-covalent)

F1D.1: 20 residues within 4Å: Chain A: P.8, T.10, A.37, A.38, S.39, F.70, S.71, D.72, L.73, M.74, L.86, R.88, E.99, L.102, M.105, N.106 Chain E: E.134, V.135, H.138 Ligands: SO4.2 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:A.37, A:F.70, E:V.135 Hydrogen bonds: A:A.38, A:S.39, A:D.72, A:M.74, A:N.106 Water bridges: A:A.75 F1D.7: 20 residues within 4Å: Chain B: P.8, T.10, A.37, A.38, S.39, P.40, F.70, S.71, D.72, L.73, M.74, L.86, R.88, E.99, L.102, M.105, N.106 Chain D: E.134, V.135, H.138 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.10, B:A.37, B:F.70, B:F.70 Hydrogen bonds: B:A.38, B:S.39, B:D.72, B:M.74, B:N.106 Water bridges: B:A.75 F1D.11: 20 residues within 4Å: Chain A: E.134, V.135, H.138 Chain C: P.8, T.10, A.37, A.38, S.39, F.70, S.71, D.72, L.73, M.74, L.86, R.88, E.99, L.102, M.105, N.106 Ligands: SO4.12 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.37, C:F.70, A:V.135 Hydrogen bonds: C:A.38, C:S.39, C:D.72, C:M.74, C:N.106 Water bridges: C:A.75 F1D.17: 20 residues within 4Å: Chain D: P.8, T.10, A.37, A.38, S.39, P.40, F.70, S.71, D.72, L.73, M.74, L.86, R.88, E.99, L.102, M.105, N.106 Chain F: E.134, V.135, H.138 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:T.10, D:A.37, D:F.70, D:F.70 Hydrogen bonds: D:A.38, D:S.39, D:D.72, D:M.74, D:N.106 Water bridges: D:A.75 F1D.21: 20 residues within 4Å: Chain C: E.134, V.135, H.138 Chain E: P.8, T.10, A.37, A.38, S.39, F.70, S.71, D.72, L.73, M.74, L.86, R.88, E.99, L.102, M.105, N.106 Ligands: SO4.22 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:A.37, E:F.70, C:V.135 Hydrogen bonds: E:A.38, E:S.39, E:D.72, E:M.74, E:N.106 Water bridges: E:A.75 F1D.27: 20 residues within 4Å: Chain B: E.134, V.135, H.138 Chain F: P.8, T.10, A.37, A.38, S.39, P.40, F.70, S.71, D.72, L.73, M.74, L.86, R.88, E.99, L.102, M.105, N.106 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:T.10, F:A.37, F:F.70, F:F.70 Hydrogen bonds: F:A.38, F:S.39, F:D.72, F:M.74, F:N.106, B:H.138 Water bridges: F:A.75

15 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: S.39, P.40, S.41 Chain E: E.134, H.138 Ligands: F1D.1 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Salt bridges: E:H.138 Hydrogen bonds: A:S.41, A:S.41 SO4.3: 4 residues within 4Å: Chain A: H.18, R.91, S.128, S.129 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.129 Water bridges: A:F.11, A:H.18, A:H.18, A:R.91, A:S.128, A:S.129, A:S.130 Salt bridges: A:H.18, A:R.91 SO4.6: 4 residues within 4Å: Chain A: S.121, K.122 Chain B: H.104, R.107 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Salt bridges: B:H.104, B:R.107, A:K.122 Hydrogen bonds: A:R.24, A:S.121, A:K.122 Water bridges: A:R.24, A:K.122 SO4.8: 4 residues within 4Å: Chain B: H.18, R.91, S.128, S.129 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.129 Water bridges: B:R.88, B:S.128, B:S.129, B:S.130 Salt bridges: B:H.18, B:R.91 SO4.9: 4 residues within 4Å: Chain A: H.104, R.107 Chain B: S.121, K.122 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.122 Water bridges: B:R.24, B:K.122, A:H.104 Salt bridges: B:K.122, A:H.104, A:R.107 SO4.12: 6 residues within 4Å: Chain A: E.134, H.138 Chain C: S.39, P.40, S.41 Ligands: F1D.11 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Salt bridges: A:H.138 Hydrogen bonds: C:S.41, C:S.41 SO4.13: 4 residues within 4Å: Chain C: H.18, R.91, S.128, S.129 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.129 Water bridges: C:F.11, C:H.18, C:H.18, C:R.91, C:S.128, C:S.129, C:S.130 Salt bridges: C:H.18, C:R.91 SO4.16: 4 residues within 4Å: Chain C: S.121, K.122 Chain D: H.104, R.107 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain C Salt bridges: D:H.104, D:R.107, C:K.122 Hydrogen bonds: C:R.24, C:S.121, C:K.122 Water bridges: C:R.24, C:K.122 SO4.18: 4 residues within 4Å: Chain D: H.18, R.91, S.128, S.129 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.129 Water bridges: D:R.88, D:S.128, D:S.129, D:S.130 Salt bridges: D:H.18, D:R.91 SO4.19: 4 residues within 4Å: Chain C: H.104, R.107 Chain D: S.121, K.122 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Water bridges: C:H.104, D:R.24, D:K.122 Salt bridges: C:H.104, C:R.107, D:K.122 Hydrogen bonds: D:K.122 SO4.22: 6 residues within 4Å: Chain C: E.134, H.138 Chain E: S.39, P.40, S.41 Ligands: F1D.21 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain E Salt bridges: C:H.138 Hydrogen bonds: E:S.41, E:S.41 SO4.23: 4 residues within 4Å: Chain E: H.18, R.91, S.128, S.129 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.129 Water bridges: E:F.11, E:H.18, E:H.18, E:R.91, E:S.128, E:S.129, E:S.130 Salt bridges: E:H.18, E:R.91 SO4.26: 4 residues within 4Å: Chain E: S.121, K.122 Chain F: H.104, R.107 8 PLIP interactions: 2 interactions with chain F, 6 interactions with chain E Salt bridges: F:H.104, F:R.107, E:K.122 Hydrogen bonds: E:R.24, E:S.121, E:K.122 Water bridges: E:R.24, E:K.122 SO4.28: 4 residues within 4Å: Chain F: H.18, R.91, S.128, S.129 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:S.129 Water bridges: F:T.10, F:R.88, F:S.128, F:S.129, F:S.130 Salt bridges: F:H.18, F:R.91 SO4.29: 4 residues within 4Å: Chain E: H.104, R.107 Chain F: S.121, K.122 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain F Salt bridges: E:H.104, E:R.107, F:K.122 Hydrogen bonds: F:K.122 Water bridges: F:R.24, F:K.122

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: H.108, L.109, P.111 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.109 PEG.14: 3 residues within 4Å: Chain C: H.108, L.109, P.111 1 PLIP interactions: 1 interactions with chain C Water bridges: C:L.109 PEG.24: 3 residues within 4Å: Chain E: H.108, L.109, P.111 1 PLIP interactions: 1 interactions with chain E Water bridges: E:L.109

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 7 residues within 4Å: Chain A: N.16, I.19, D.20, T.23, R.24, Q.27, W.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.20, A:Q.27 Water bridges: A:N.16, A:N.16 PG4.10: 7 residues within 4Å: Chain B: N.16, I.19, D.20, T.23, R.24, Q.27, W.124 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.27 Water bridges: B:N.16 PG4.15: 7 residues within 4Å: Chain C: N.16, I.19, D.20, T.23, R.24, Q.27, W.124 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.27 Water bridges: C:N.16, C:N.16 PG4.20: 7 residues within 4Å: Chain D: N.16, I.19, D.20, T.23, R.24, Q.27, W.124 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.27 Water bridges: D:N.16, D:D.20, D:D.20 PG4.25: 7 residues within 4Å: Chain E: N.16, I.19, D.20, T.23, R.24, Q.27, W.124 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.20, E:Q.27 Water bridges: E:N.16, E:N.16 PG4.30: 7 residues within 4Å: Chain F: N.16, I.19, D.20, T.23, R.24, Q.27, W.124 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.27 Water bridges: F:N.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skepper, C.K. et al., Discovery and Optimization of Phosphopantetheine Adenylyltransferase Inhibitors with Gram-Negative Antibacterial Activity. J. Med. Chem. (2018)

Release Date

2018-04-04

Peptides

Phosphopantetheine adenylyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Phosphopantetheine adenylyltransferase

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