Fluorine in PDB 4lp0: Crystal Structure of A Topoisomerase Atp Inhibitor

The structure of Crystal Structure of A Topoisomerase Atp Inhibitor, PDB code: 4lp0 was solved by G.S.Basarab, J.I.Manchester, S.Bist, P.A.Boriack-Sjodin, B.Dangel, R.Illingsworth, M.Uria-Nickelsen, B.A.Sherer, S.Sriram, A.E.Eakin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.67 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.875, 94.333, 62.270, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20.2

The binding sites of Fluorine atom in the Crystal Structure of A Topoisomerase Atp Inhibitor (pdb code 4lp0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of A Topoisomerase Atp Inhibitor, PDB code: 4lp0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of A Topoisomerase Atp Inhibitor


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 A Topoisomerase Atp Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:38.2 occ:1.00 F28 A:1YM301 0.0 38.2 1.0 C27 A:1YM301 1.4 40.1 1.0 F29 A:1YM301 2.2 47.6 1.0 F30 A:1YM301 2.3 46.2 1.0 C24 A:1YM301 2.4 34.8 1.0 N23 A:1YM301 2.9 30.9 1.0 CD A:PRO84 3.1 24.0 1.0 CG A:PRO84 3.2 29.0 1.0 CD1 A:ILE98 3.5 26.5 1.0 C25 A:1YM301 3.6 32.9 1.0 CG2 A:THR94 4.1 26.5 1.0 C22 A:1YM301 4.2 25.5 1.0 CG1 A:ILE98 4.3 24.4 1.0 CB A:PRO84 4.4 27.9 1.0 N A:PRO84 4.6 22.1 1.0 C14 A:1YM301 4.7 28.2 1.0 C15 A:1YM301 4.7 29.0 1.0 S26 A:1YM301 4.8 36.2 1.0 C13 A:1YM301 4.9 22.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of A Topoisomerase Atp Inhibitor


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 A Topoisomerase Atp Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:47.6 occ:1.00 F29 A:1YM301 0.0 47.6 1.0 C27 A:1YM301 1.4 40.1 1.0 F30 A:1YM301 2.2 46.2 1.0 F28 A:1YM301 2.2 38.2 1.0 C24 A:1YM301 2.3 34.8 1.0 N23 A:1YM301 3.0 30.9 1.0 C25 A:1YM301 3.3 32.9 1.0 C19 A:1YM301 3.5 36.8 1.0 O20 A:1YM301 3.7 41.3 1.0 C15 A:1YM301 3.7 29.0 1.0 C14 A:1YM301 3.9 28.2 1.0 O21 A:1YM301 4.0 40.4 1.0 C22 A:1YM301 4.1 25.5 1.0 C16 A:1YM301 4.5 26.9 1.0 S26 A:1YM301 4.6 36.2 1.0 CG A:PRO84 4.7 29.0 1.0 C13 A:1YM301 4.7 22.9 1.0 CD A:PRO84 4.8 24.0 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of A Topoisomerase Atp Inhibitor


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 A Topoisomerase Atp Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:46.2 occ:1.00 F30 A:1YM301 0.0 46.2 1.0 C27 A:1YM301 1.4 40.1 1.0 F29 A:1YM301 2.2 47.6 1.0 C24 A:1YM301 2.3 34.8 1.0 F28 A:1YM301 2.3 38.2 1.0 C25 A:1YM301 2.6 32.9 1.0 N23 A:1YM301 3.5 30.9 1.0 CD1 A:ILE98 3.7 26.5 1.0 CG1 A:ILE98 3.7 24.4 1.0 S26 A:1YM301 4.3 36.2 1.0 C22 A:1YM301 4.6 25.5 1.0

G.S.Basarab, J.I.Manchester, S.Bist, P.A.Boriack-Sjodin, B.Dangel, R.Illingworth, B.A.Sherer, S.Sriram, M.Uria-Nickelsen, A.E.Eakin. Fragment-to-Hit-to-Lead Discovery of A Novel Pyridylurea Scaffold of Atp Competitive Dual Targeting Type II Topoisomerase Inhibiting Antibacterial Agents. J.Med.Chem. V. 56 8712 2013.
ISSN: ISSN 0022-2623
PubMed: 24098982
DOI: 10.1021/JM401208B