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Fluorine in PDB 6ccs: Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol

Enzymatic activity of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol

All present enzymatic activity of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol:
2.7.7.3;

Protein crystallography data

The structure of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol, PDB code: 6ccs was solved by M.Mamo, B.A.Appleton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.69 / 2.06
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 134.993, 134.993, 134.993, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol (pdb code 6ccs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol, PDB code: 6ccs:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6ccs

Go back to Fluorine Binding Sites List in 6ccs
Fluorine binding site 1 out of 6 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:41.5
occ:1.00
 F1 A:EXD201 0.0 41.5 1.0
C7 A:EXD201 1.3 39.3 1.0
F2 A:EXD201 2.1 38.2 1.0
F A:EXD201 2.2 42.2 1.0
C5 A:EXD201 2.3 32.2 1.0
N1 A:EXD201 3.0 28.4 1.0
N A:EXD201 3.3 34.3 1.0
O A:HOH338 3.5 31.4 1.0
O A:HOH380 3.7 64.0 1.0
CE A:MET74 3.7 41.8 1.0
CE2 A:PHE70 3.9 30.3 1.0
CB A:ALA37 4.0 24.3 1.0
C6 A:EXD201 4.1 30.6 1.0
O A:ASP72 4.2 29.2 1.0
CZ A:PHE70 4.2 27.6 1.0
N A:MET74 4.2 29.9 1.0
CB A:MET74 4.2 32.4 1.0
O A:HOH313 4.2 35.4 1.0
C4 A:EXD201 4.3 34.8 1.0
CA A:MET74 4.8 29.1 1.0
CG A:MET74 4.8 38.2 1.0
CD2 A:PHE70 5.0 27.7 1.0

Fluorine binding site 2 out of 6 in 6ccs

Go back to Fluorine Binding Sites List in 6ccs
Fluorine binding site 2 out of 6 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:38.2
occ:1.00
 F2 A:EXD201 0.0 38.2 1.0
C7 A:EXD201 1.3 39.3 1.0
F A:EXD201 2.1 42.2 1.0
F1 A:EXD201 2.1 41.5 1.0
C5 A:EXD201 2.4 32.2 1.0
O A:ASP72 2.8 29.2 1.0
N1 A:EXD201 2.9 28.4 1.0
O A:HOH338 3.0 31.4 1.0
N A:EXD201 3.5 34.3 1.0
C A:ASP72 3.7 30.5 1.0
CA A:LEU73 3.8 24.8 1.0
N A:MET74 3.9 29.9 1.0
O A:HOH313 4.0 35.4 1.0
N A:LEU73 4.1 26.7 1.0
C6 A:EXD201 4.2 30.6 1.0
C A:LEU73 4.2 28.2 1.0
CE2 A:PHE70 4.4 30.3 1.0
C4 A:EXD201 4.5 34.8 1.0
O A:SER71 4.6 35.4 1.0
O A:HOH380 4.8 64.0 1.0
CA A:MET74 4.9 29.1 1.0
O4 A:SO4202 4.9 47.4 1.0
C A:SER71 5.0 32.9 1.0
CD2 A:PHE70 5.0 27.7 1.0

Fluorine binding site 3 out of 6 in 6ccs

Go back to Fluorine Binding Sites List in 6ccs
Fluorine binding site 3 out of 6 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:42.2
occ:1.00
 F A:EXD201 0.0 42.2 1.0
C7 A:EXD201 1.3 39.3 1.0
F2 A:EXD201 2.1 38.2 1.0
F1 A:EXD201 2.2 41.5 1.0
C5 A:EXD201 2.3 32.2 1.0
N A:EXD201 2.8 34.3 1.0
O A:HOH380 3.1 64.0 1.0
N1 A:EXD201 3.6 28.4 1.0
O A:HOH313 3.7 35.4 1.0
O3 A:SO4202 3.8 44.3 1.0
O4 A:SO4202 4.0 47.4 1.0
C4 A:EXD201 4.1 34.8 1.0
O A:HOH338 4.1 31.4 1.0
C6 A:EXD201 4.4 30.6 1.0
S A:SO4202 4.5 45.6 1.0
O A:ASP72 4.9 29.2 1.0

Fluorine binding site 4 out of 6 in 6ccs

Go back to Fluorine Binding Sites List in 6ccs
Fluorine binding site 4 out of 6 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:53.9
occ:1.00
 F1 B:EXD201 0.0 53.9 1.0
C7 B:EXD201 1.3 51.1 1.0
F2 B:EXD201 2.1 53.9 1.0
F B:EXD201 2.2 49.0 1.0
C5 B:EXD201 2.3 46.1 1.0
N1 B:EXD201 3.0 43.4 1.0
O B:ASP72 3.4 36.4 0.3
N B:EXD201 3.4 45.1 1.0
O B:ASP72 3.4 35.3 0.7
CA B:LEU73 3.5 31.4 1.0
O B:HOH322 3.7 37.6 1.0
N B:MET74 3.9 29.0 0.5
C B:ASP72 4.0 37.2 0.3
C B:ASP72 4.0 36.7 0.7
N B:MET74 4.0 30.7 0.5
N B:LEU73 4.0 33.2 1.0
C6 B:EXD201 4.1 41.5 1.0
C B:LEU73 4.2 33.5 1.0
C4 B:EXD201 4.4 41.5 1.0
CD1 B:LEU73 4.4 35.8 1.0
CB B:LEU73 4.6 31.4 1.0

Fluorine binding site 5 out of 6 in 6ccs

Go back to Fluorine Binding Sites List in 6ccs
Fluorine binding site 5 out of 6 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:53.9
occ:1.00
 F2 B:EXD201 0.0 53.9 1.0
C7 B:EXD201 1.3 51.1 1.0
F1 B:EXD201 2.1 53.9 1.0
F B:EXD201 2.2 49.0 1.0
C5 B:EXD201 2.3 46.1 1.0
N B:EXD201 2.8 45.1 1.0
N1 B:EXD201 3.6 43.4 1.0
C4 B:EXD201 4.1 41.5 1.0
C6 B:EXD201 4.4 41.5 1.0
O B:HOH322 4.6 37.6 1.0
O B:HOH344 4.8 66.3 1.0

Fluorine binding site 6 out of 6 in 6ccs

Go back to Fluorine Binding Sites List in 6ccs
Fluorine binding site 6 out of 6 in the Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of E.Coli Phosphopantetheine Adenylyltransferase (Ppat/Coad) in Complex with 2-(Trifluoromethyl)-1H-Benzo[D]Imidazol- 4-Ol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:49.0
occ:1.00
 F B:EXD201 0.0 49.0 1.0
C7 B:EXD201 1.3 51.1 1.0
F2 B:EXD201 2.2 53.9 1.0
F1 B:EXD201 2.2 53.9 1.0
C5 B:EXD201 2.3 46.1 1.0
N1 B:EXD201 2.8 43.4 1.0
N B:EXD201 3.5 45.1 1.0
O B:HOH322 3.6 37.6 1.0
N B:MET74 3.9 29.0 0.5
N B:MET74 3.9 30.7 0.5
CE2 B:PHE70 4.0 30.5 1.0
C6 B:EXD201 4.1 41.5 1.0
CB B:MET74 4.1 31.7 0.5
CB B:MET74 4.1 28.6 0.5
O B:ASP72 4.1 36.4 0.3
O B:ASP72 4.1 35.3 0.7
CE B:MET74 4.2 35.1 0.5
CZ B:PHE70 4.2 27.7 1.0
C4 B:EXD201 4.4 41.5 1.0
CA B:MET74 4.5 27.2 0.5
CA B:MET74 4.5 29.7 0.5
C B:LEU73 4.7 33.5 1.0
CA B:LEU73 4.7 31.4 1.0
CG B:MET74 4.8 34.8 0.5
CB B:ALA37 4.9 40.2 1.0
CG B:MET74 5.0 30.6 0.5

Reference:

R.J.Moreau, C.K.Skepper, B.A.Appleton, A.Blechschmidt, C.J.Balibar, B.M.Benton, J.E.Drumm, B.Y.Feng, M.Geng, C.Li, M.K.Lindvall, A.Lingel, Y.Lu, M.Mamo, W.Mergo, V.Polyakov, T.M.Smith, K.Takeoka, K.Uehara, L.Wang, J.R.Wei, A.H.Weiss, L.Xie, W.Xu, Q.Zhang, J.De Vicente. Fragment-Based Drug Discovery of Inhibitors of Phosphopantetheine Adenylyltransferase From Gram-Negative Bacteria. J. Med. Chem. V. 61 3309 2018.
ISSN: ISSN 1520-4804
PubMed: 29498517
DOI: 10.1021/ACS.JMEDCHEM.7B01691
Page generated: Tue Jul 15 10:21:30 2025

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