- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.06 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x F6D: (3R)-3-[(7-{[(2S)-2-amino-2-(2-methoxyphenyl)ethyl]amino}-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino]-3-(3-chlorophenyl)propanenitrile(Non-covalent)
- 27 x SO4: SULFATE ION(Non-functional Binders)
SO4.2: 6 residues within 4Å:- Chain A: G.9, T.10, K.42, R.88
- Ligands: F6D.1, DMS.5
Ligand excluded by PLIPSO4.3: 5 residues within 4Å:- Chain A: H.18, R.91, S.128, S.129
- Ligands: DMS.5
Ligand excluded by PLIPSO4.4: 7 residues within 4Å:- Chain A: S.39, P.40, S.41
- Chain C: E.134, R.137, H.138
- Ligands: F6D.1
Ligand excluded by PLIPSO4.7: 5 residues within 4Å:- Chain A: R.24, S.121, K.122
- Chain B: H.104, R.107
Ligand excluded by PLIPSO4.9: 5 residues within 4Å:- Chain B: G.9, T.10, R.88
- Ligands: F6D.8, DMS.13
Ligand excluded by PLIPSO4.10: 5 residues within 4Å:- Chain B: P.40, S.41
- Chain F: E.134, H.138
- Ligands: F6D.8
Ligand excluded by PLIPSO4.11: 5 residues within 4Å:- Chain B: H.18, R.91, S.128, S.129
- Ligands: DMS.13
Ligand excluded by PLIPSO4.12: 4 residues within 4Å:- Chain A: H.104, R.107
- Chain B: S.121, K.122
Ligand excluded by PLIPSO4.14: 5 residues within 4Å:- Chain B: K.42, S.130, K.133, E.134, R.137
Ligand excluded by PLIPSO4.18: 6 residues within 4Å:- Chain C: G.9, T.10, K.42, R.88
- Ligands: F6D.17, DMS.21
Ligand excluded by PLIPSO4.19: 5 residues within 4Å:- Chain C: H.18, R.91, S.128, S.129
- Ligands: DMS.21
Ligand excluded by PLIPSO4.20: 7 residues within 4Å:- Chain C: S.39, P.40, S.41
- Chain E: E.134, R.137, H.138
- Ligands: F6D.17
Ligand excluded by PLIPSO4.23: 5 residues within 4Å:- Chain C: R.24, S.121, K.122
- Chain D: H.104, R.107
Ligand excluded by PLIPSO4.25: 5 residues within 4Å:- Chain D: G.9, T.10, R.88
- Ligands: F6D.24, DMS.29
Ligand excluded by PLIPSO4.26: 5 residues within 4Å:- Chain B: E.134, H.138
- Chain D: P.40, S.41
- Ligands: F6D.24
Ligand excluded by PLIPSO4.27: 5 residues within 4Å:- Chain D: H.18, R.91, S.128, S.129
- Ligands: DMS.29
Ligand excluded by PLIPSO4.28: 4 residues within 4Å:- Chain C: H.104, R.107
- Chain D: S.121, K.122
Ligand excluded by PLIPSO4.30: 5 residues within 4Å:- Chain D: K.42, S.130, K.133, E.134, R.137
Ligand excluded by PLIPSO4.34: 6 residues within 4Å:- Chain E: G.9, T.10, K.42, R.88
- Ligands: F6D.33, DMS.37
Ligand excluded by PLIPSO4.35: 5 residues within 4Å:- Chain E: H.18, R.91, S.128, S.129
- Ligands: DMS.37
Ligand excluded by PLIPSO4.36: 7 residues within 4Å:- Chain A: E.134, R.137, H.138
- Chain E: S.39, P.40, S.41
- Ligands: F6D.33
Ligand excluded by PLIPSO4.39: 5 residues within 4Å:- Chain E: R.24, S.121, K.122
- Chain F: H.104, R.107
Ligand excluded by PLIPSO4.41: 5 residues within 4Å:- Chain F: G.9, T.10, R.88
- Ligands: F6D.40, DMS.45
Ligand excluded by PLIPSO4.42: 5 residues within 4Å:- Chain D: E.134, H.138
- Chain F: P.40, S.41
- Ligands: F6D.40
Ligand excluded by PLIPSO4.43: 5 residues within 4Å:- Chain F: H.18, R.91, S.128, S.129
- Ligands: DMS.45
Ligand excluded by PLIPSO4.44: 4 residues within 4Å:- Chain E: H.104, R.107
- Chain F: S.121, K.122
Ligand excluded by PLIPSO4.46: 5 residues within 4Å:- Chain F: K.42, S.130, K.133, E.134, R.137
Ligand excluded by PLIP- 12 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.5: 8 residues within 4Å:- Chain A: Y.7, P.8, G.9, R.88, G.89
- Ligands: SO4.2, SO4.3, DMS.6
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.7, A:G.89
- Salt bridges: A:E.99
DMS.6: 8 residues within 4Å:- Chain A: Y.7, G.17, H.18, I.21, G.89, R.91, P.120
- Ligands: DMS.5
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.91
DMS.13: 8 residues within 4Å:- Chain B: Y.7, P.8, G.9, R.88, G.89
- Ligands: SO4.9, SO4.11, DMS.15
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Y.7, B:G.89
- Salt bridges: B:E.99
DMS.15: 8 residues within 4Å:- Chain B: Y.7, G.17, H.18, I.21, G.89, R.91, P.120
- Ligands: DMS.13
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:R.91
DMS.21: 8 residues within 4Å:- Chain C: Y.7, P.8, G.9, R.88, G.89
- Ligands: SO4.18, SO4.19, DMS.22
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:G.89
- Salt bridges: C:E.99
DMS.22: 8 residues within 4Å:- Chain C: Y.7, G.17, H.18, I.21, G.89, R.91, P.120
- Ligands: DMS.21
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:R.91
DMS.29: 8 residues within 4Å:- Chain D: Y.7, P.8, G.9, R.88, G.89
- Ligands: SO4.25, SO4.27, DMS.31
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:G.89
- Salt bridges: D:E.99
DMS.31: 8 residues within 4Å:- Chain D: Y.7, G.17, H.18, I.21, G.89, R.91, P.120
- Ligands: DMS.29
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:R.91
DMS.37: 8 residues within 4Å:- Chain E: Y.7, P.8, G.9, R.88, G.89
- Ligands: SO4.34, SO4.35, DMS.38
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:G.89
- Salt bridges: E:E.99
DMS.38: 8 residues within 4Å:- Chain E: Y.7, G.17, H.18, I.21, G.89, R.91, P.120
- Ligands: DMS.37
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:R.91
DMS.45: 8 residues within 4Å:- Chain F: Y.7, P.8, G.9, R.88, G.89
- Ligands: SO4.41, SO4.43, DMS.47
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:Y.7, F:G.89
- Salt bridges: F:E.99
DMS.47: 8 residues within 4Å:- Chain F: Y.7, G.17, H.18, I.21, G.89, R.91, P.120
- Ligands: DMS.45
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:R.91
- 3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
PG4.16: 5 residues within 4Å:- Chain B: N.16, I.19, D.20, T.23, W.124
No protein-ligand interaction detected (PLIP)PG4.32: 5 residues within 4Å:- Chain D: N.16, I.19, D.20, T.23, W.124
No protein-ligand interaction detected (PLIP)PG4.48: 5 residues within 4Å:- Chain F: N.16, I.19, D.20, T.23, W.124
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:D.20
- 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
AB
BC
AD
BE
AF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.06 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x F6D: (3R)-3-[(7-{[(2S)-2-amino-2-(2-methoxyphenyl)ethyl]amino}-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)amino]-3-(3-chlorophenyl)propanenitrile(Non-covalent)
- 27 x SO4: SULFATE ION(Non-functional Binders)
- 12 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 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
AB
BC
AD
BE
AF
B