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: Sun Dec 13 12:46:31 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy