Fluorine in PDB 5g48: H.Pylori Beta Clamp in Complex with Diflunisal

The structure of H.Pylori Beta Clamp in Complex with Diflunisal, PDB code: 5g48 was solved by P.Pandey, S.Gourinath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.19 / 2.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.311, 66.372, 89.119, 90.00, 115.96, 90.00
R / Rfree (%)	23.5 / 25.5

The binding sites of Fluorine atom in the H.Pylori Beta Clamp in Complex with Diflunisal (pdb code 5g48). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the H.Pylori Beta Clamp in Complex with Diflunisal, PDB code: 5g48:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the H.Pylori Beta Clamp in Complex with Diflunisal


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of H.Pylori Beta Clamp in Complex with Diflunisal within 5.0Å range: probe atom residue distance (Å) B Occ A:F1375 b:42.1 occ:1.00 FAT A:1FL1375 0.0 42.1 1.0 CAN A:1FL1375 1.3 43.3 1.0 CAM A:1FL1375 2.4 42.8 1.0 CAO A:1FL1375 2.5 44.5 1.0 CAP A:1FL1375 2.9 46.2 1.0 OG1 A:THR173 2.9 36.7 1.0 CAQ A:1FL1375 3.0 47.2 1.0 C A:ARG177 3.1 36.9 1.0 O A:ARG177 3.1 36.3 1.0 C A:THR175 3.1 39.2 1.0 O A:THR175 3.3 39.7 1.0 N A:LEU178 3.4 37.2 1.0 CA A:THR175 3.5 39.2 1.0 N A:ARG177 3.5 37.5 1.0 N A:LYS176 3.6 39.0 1.0 CB A:LEU178 3.6 38.2 1.0 CAF A:1FL1375 3.6 43.1 1.0 CA A:ARG177 3.6 36.8 1.0 C A:LYS176 3.7 38.4 1.0 CAH A:1FL1375 3.7 43.9 1.0 N A:THR175 3.8 38.4 1.0 CA A:LEU178 3.9 37.6 1.0 CAI A:1FL1375 4.0 46.9 1.0 CA A:LYS176 4.1 39.1 1.0 CAR A:1FL1375 4.2 48.0 1.0 CAG A:1FL1375 4.2 43.6 1.0 O A:LYS176 4.2 38.5 1.0 CB A:THR173 4.3 36.9 1.0 CD1 A:LEU178 4.7 39.5 1.0 O A:LEU368 4.7 38.9 1.0 FAE A:1FL1375 4.7 42.6 1.0 CG A:LEU178 4.7 38.8 1.0 OD1 A:ASP174 4.8 35.5 1.0 CB A:THR175 4.9 39.8 1.0 N A:ASP174 4.9 36.4 1.0 C A:ASP174 4.9 37.8 1.0 CAJ A:1FL1375 4.9 48.3 1.0

Fluorine binding site 2 out of 4 in the H.Pylori Beta Clamp in Complex with Diflunisal


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of H.Pylori Beta Clamp in Complex with Diflunisal within 5.0Å range: probe atom residue distance (Å) B Occ A:F1375 b:42.6 occ:1.00 FAE A:1FL1375 0.0 42.6 1.0 CAF A:1FL1375 1.3 43.1 1.0 CAM A:1FL1375 2.4 42.8 1.0 CAG A:1FL1375 2.4 43.6 1.0 N A:MET370 3.1 42.3 1.0 C A:MET369 3.1 41.4 1.0 CB A:PRO347 3.4 38.9 1.0 N A:MET369 3.5 39.8 1.0 CA A:MET369 3.6 40.9 1.0 O A:MET369 3.6 41.0 1.0 CG A:LEU368 3.6 39.3 1.0 CAN A:1FL1375 3.6 43.3 1.0 CAH A:1FL1375 3.7 43.9 1.0 CG A:MET370 3.7 46.2 1.0 CD2 A:LEU368 3.7 39.9 1.0 CA A:MET370 3.8 43.4 1.0 C A:LEU368 3.8 38.7 1.0 O A:LEU368 3.9 38.9 1.0 SD A:MET370 3.9 48.7 1.0 CG A:PRO347 4.0 39.6 1.0 O A:LYS176 4.1 38.5 1.0 CAO A:1FL1375 4.2 44.5 1.0 CB A:MET370 4.2 44.7 1.0 CA A:PRO347 4.3 38.6 1.0 CB A:LEU368 4.5 38.5 1.0 CD1 A:LEU368 4.7 39.5 1.0 FAT A:1FL1375 4.7 42.1 1.0 CA A:LEU368 4.7 38.0 1.0 C A:LYS176 4.9 38.4 1.0

Fluorine binding site 3 out of 4 in the H.Pylori Beta Clamp in Complex with Diflunisal


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of H.Pylori Beta Clamp in Complex with Diflunisal within 5.0Å range: probe atom residue distance (Å) B Occ B:F1375 b:36.9 occ:1.00 FAT B:1FL1375 0.0 36.9 1.0 CAN B:1FL1375 1.3 36.8 1.0 CAM B:1FL1375 2.4 36.9 1.0 CAO B:1FL1375 2.5 37.0 1.0 OG1 B:THR173 2.9 32.7 1.0 CAP B:1FL1375 3.0 37.4 1.0 CAQ B:1FL1375 3.1 37.3 1.0 C B:THR175 3.1 35.9 1.0 C B:ARG177 3.3 34.1 1.0 O B:THR175 3.3 36.5 1.0 O B:ARG177 3.3 33.5 1.0 CA B:THR175 3.4 35.2 1.0 N B:LYS176 3.5 36.0 1.0 N B:LEU178 3.5 34.2 1.0 CB B:LEU178 3.6 34.8 1.0 CAF B:1FL1375 3.6 37.0 1.0 N B:ARG177 3.6 34.6 1.0 CAH B:1FL1375 3.7 36.5 1.0 CA B:ARG177 3.8 34.1 1.0 C B:LYS176 3.8 35.5 1.0 N B:THR175 3.8 34.1 1.0 CA B:LEU178 4.0 34.1 1.0 CAI B:1FL1375 4.1 37.7 1.0 CA B:LYS176 4.1 36.2 1.0 CAG B:1FL1375 4.2 36.6 1.0 CB B:THR173 4.2 32.7 1.0 CAR B:1FL1375 4.2 37.5 1.0 O B:LYS176 4.3 35.2 1.0 CD1 B:LEU178 4.6 36.1 1.0 O B:LEU368 4.7 36.8 1.0 FAE B:1FL1375 4.7 37.9 1.0 CG B:LEU178 4.7 35.6 1.0 CB B:THR175 4.8 35.7 1.0 CG2 B:THR173 4.9 33.0 1.0 C B:ASP174 5.0 33.4 1.0 OD1 B:ASP174 5.0 32.3 1.0

Fluorine binding site 4 out of 4 in the H.Pylori Beta Clamp in Complex with Diflunisal


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of H.Pylori Beta Clamp in Complex with Diflunisal within 5.0Å range: probe atom residue distance (Å) B Occ B:F1375 b:37.9 occ:1.00 FAE B:1FL1375 0.0 37.9 1.0 CAF B:1FL1375 1.3 37.0 1.0 CAM B:1FL1375 2.4 36.9 1.0 CAG B:1FL1375 2.4 36.6 1.0 N B:MET370 3.1 40.5 1.0 C B:MET369 3.2 39.6 1.0 CB B:PRO347 3.4 39.8 1.0 CG B:LEU368 3.5 37.2 1.0 N B:MET369 3.5 38.0 1.0 CG B:MET370 3.6 44.5 1.0 CAN B:1FL1375 3.6 36.8 1.0 CA B:MET369 3.6 39.1 1.0 O B:MET369 3.7 39.2 1.0 CAH B:1FL1375 3.7 36.5 1.0 CG B:PRO347 3.7 40.4 1.0 CD2 B:LEU368 3.7 37.6 1.0 CA B:MET370 3.7 42.0 1.0 C B:LEU368 3.9 36.9 1.0 O B:LEU368 4.0 36.8 1.0 SD B:MET370 4.0 46.9 1.0 CA B:PRO347 4.1 39.4 1.0 CAO B:1FL1375 4.2 37.0 1.0 CB B:MET370 4.2 43.2 1.0 O B:LYS176 4.4 35.2 1.0 CB B:LEU368 4.4 36.7 1.0 CD1 B:LEU368 4.4 37.4 1.0 FAT B:1FL1375 4.7 36.9 1.0 CA B:LEU368 4.7 36.2 1.0 CD B:PRO347 4.9 40.7 1.0

P.Pandey, V.Verma, G.Gautam, N.Kumari, S.K.Dhar, S.Gourinath. Targeting the Beta-Clamp in Helicobacter Pylori with Fda-Approved Drugs Reveals Micromolar Inhibition By Diflunisal. Febs Lett. V. 591 2311 2017.
ISSN: ISSN 1873-3468
PubMed: 28656718
DOI: 10.1002/1873-3468.12734