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Fluorine in PDB 4ksg: Dna Gyrase Atp Binding Domain of Enterococcus Faecalis in Complex with A Small Molecule Inhibitor (4-[(1S,5R,6R)-6-Amino-1-Methyl-3- Azabicyclo[3.2.0]Hept-3-Yl]-6-Fluoro-N-Methyl-2-[(2-Methylpyrimidin- 5-Yl)Oxy]-9H-Pyrimido[4,5-B]Indol-8-Amine)

Enzymatic activity of Dna Gyrase Atp Binding Domain of Enterococcus Faecalis in Complex with A Small Molecule Inhibitor (4-[(1S,5R,6R)-6-Amino-1-Methyl-3- Azabicyclo[3.2.0]Hept-3-Yl]-6-Fluoro-N-Methyl-2-[(2-Methylpyrimidin- 5-Yl)Oxy]-9H-Pyrimido[4,5-B]Indol-8-Amine)

All present enzymatic activity of Dna Gyrase Atp Binding Domain of Enterococcus Faecalis in Complex with A Small Molecule Inhibitor (4-[(1S,5R,6R)-6-Amino-1-Methyl-3- Azabicyclo[3.2.0]Hept-3-Yl]-6-Fluoro-N-Methyl-2-[(2-Methylpyrimidin- 5-Yl)Oxy]-9H-Pyrimido[4,5-B]Indol-8-Amine):
5.99.1.3;

Protein crystallography data

The structure of Dna Gyrase Atp Binding Domain of Enterococcus Faecalis in Complex with A Small Molecule Inhibitor (4-[(1S,5R,6R)-6-Amino-1-Methyl-3- Azabicyclo[3.2.0]Hept-3-Yl]-6-Fluoro-N-Methyl-2-[(2-Methylpyrimidin- 5-Yl)Oxy]-9H-Pyrimido[4,5-B]Indol-8-Amine), PDB code: 4ksg was solved by D.C Bensen, S.Akers-Rodriguez, L.W.Tari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.76 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.680, 58.660, 65.990, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dna Gyrase Atp Binding Domain of Enterococcus Faecalis in Complex with A Small Molecule Inhibitor (4-[(1S,5R,6R)-6-Amino-1-Methyl-3- Azabicyclo[3.2.0]Hept-3-Yl]-6-Fluoro-N-Methyl-2-[(2-Methylpyrimidin- 5-Yl)Oxy]-9H-Pyrimido[4,5-B]Indol-8-Amine) (pdb code 4ksg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Dna Gyrase Atp Binding Domain of Enterococcus Faecalis in Complex with A Small Molecule Inhibitor (4-[(1S,5R,6R)-6-Amino-1-Methyl-3- Azabicyclo[3.2.0]Hept-3-Yl]-6-Fluoro-N-Methyl-2-[(2-Methylpyrimidin- 5-Yl)Oxy]-9H-Pyrimido[4,5-B]Indol-8-Amine), PDB code: 4ksg:

Fluorine binding site 1 out of 1 in 4ksg

Go back to Fluorine Binding Sites List in 4ksg
Fluorine binding site 1 out of 1 in the Dna Gyrase Atp Binding Domain of Enterococcus Faecalis in Complex with A Small Molecule Inhibitor (4-[(1S,5R,6R)-6-Amino-1-Methyl-3- Azabicyclo[3.2.0]Hept-3-Yl]-6-Fluoro-N-Methyl-2-[(2-Methylpyrimidin- 5-Yl)Oxy]-9H-Pyrimido[4,5-B]Indol-8-Amine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dna Gyrase Atp Binding Domain of Enterococcus Faecalis in Complex with A Small Molecule Inhibitor (4-[(1S,5R,6R)-6-Amino-1-Methyl-3- Azabicyclo[3.2.0]Hept-3-Yl]-6-Fluoro-N-Methyl-2-[(2-Methylpyrimidin- 5-Yl)Oxy]-9H-Pyrimido[4,5-B]Indol-8-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:13.7
occ:1.00
 F31 A:920301 0.0 13.7 1.0
C6 A:920301 1.3 12.7 1.0
C1 A:920301 2.4 12.5 1.0
C5 A:920301 2.4 12.7 1.0
ND2 A:ASN48 3.5 14.4 1.0
CE1 A:PHE97 3.5 12.0 1.0
CB A:SER122 3.6 15.0 1.0
CZ A:PHE97 3.6 11.8 1.0
C4 A:920301 3.6 12.4 1.0
C2 A:920301 3.7 12.2 1.0
CG A:ASN48 3.8 13.7 1.0
CD1 A:ILE45 4.0 11.0 1.0
CB A:ASN48 4.0 12.7 1.0
CG2 A:VAL169 4.1 9.1 1.0
C3 A:920301 4.2 12.3 1.0
CG2 A:ILE45 4.4 11.1 1.0
OG A:SER122 4.4 16.8 1.0
OD1 A:ASN48 4.4 14.5 1.0
CG1 A:VAL96 4.5 13.6 1.0
CA A:SER122 4.7 14.1 1.0
CD1 A:PHE97 4.7 12.1 1.0
O A:ILE45 4.8 11.3 1.0
CE2 A:PHE97 4.8 11.8 1.0
N32 A:920301 4.8 12.3 1.0
CA A:ILE45 4.8 11.4 1.0
CD1 A:ILE80 4.9 13.2 1.0

Reference:

L.W.Tari, D.C.Bensen, J.Finn. A New Class of Type Iia Topoisomerase Inhibitors with Broad-Spectrum Antibacterial Activity To Be Published.
Page generated: Mon Jul 14 22:54:50 2025

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