Fluorine in PDB 1dvy: Crystal Structure of Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid

The structure of Crystal Structure of Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid, PDB code: 1dvy was solved by T.Klabunde, H.M.Petrassi, V.B.Oza, J.W.Kelly, J.C.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.290, 86.030, 65.230, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 20.3

The binding sites of Fluorine atom in the Crystal Structure of Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid (pdb code 1dvy). 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 Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid, PDB code: 1dvy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid


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 Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F125 b:33.3 occ:0.28 F1 A:BPD125 0.0 33.3 0.3 C1 A:BPD125 1.3 33.6 0.3 F2 A:BPD125 2.1 32.2 0.3 F3 A:BPD125 2.1 33.8 0.3 C2 A:BPD125 2.3 33.6 0.3 C7 A:BPD125 3.0 33.9 0.3 CB A:ALA108 3.3 21.2 1.0 C3 A:BPD125 3.4 34.1 0.3 C A:ALA108 3.9 18.8 1.0 N A:ALA109 4.0 17.2 1.0 CG2 A:THR119 4.1 26.2 1.0 C A:ALA109 4.2 18.1 1.0 CA A:ALA108 4.2 20.2 1.0 O A:ALA108 4.2 19.6 1.0 N A:LEU110 4.3 16.7 1.0 C6 A:BPD125 4.3 34.1 0.3 CA A:ALA109 4.4 17.9 1.0 CB A:LEU110 4.4 16.0 1.0 O A:ALA109 4.4 17.6 1.0 C4 A:BPD125 4.6 33.6 0.3 CA A:LEU110 4.8 15.9 1.0 C5 A:BPD125 5.0 34.3 0.3

Fluorine binding site 2 out of 6 in the Crystal Structure of Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid


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 Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F125 b:33.3 occ:0.28 F1 A:BPD125 0.0 33.3 0.3 C1 A:BPD125 1.3 34.0 0.3 F2 A:BPD125 2.1 33.0 0.3 F3 A:BPD125 2.1 33.6 0.3 C2 A:BPD125 2.3 33.5 0.3 C7 A:BPD125 3.0 33.9 0.3 CB B:ALA108 3.2 21.6 1.0 C3 A:BPD125 3.4 34.6 0.3 CG2 B:THR119 3.9 26.1 1.0 C B:ALA108 3.9 19.3 1.0 N B:ALA109 4.0 18.6 1.0 CA B:ALA108 4.2 21.2 1.0 O B:ALA108 4.2 22.2 1.0 C B:ALA109 4.3 18.3 1.0 C6 A:BPD125 4.3 34.2 0.3 N B:LEU110 4.4 17.3 1.0 CA B:ALA109 4.5 19.2 1.0 CB B:LEU110 4.5 17.2 1.0 O B:ALA109 4.5 19.9 1.0 C4 A:BPD125 4.6 33.7 0.3 CA B:LEU110 4.9 17.5 1.0 CB B:THR119 4.9 22.0 1.0 C5 A:BPD125 5.0 34.5 0.3

Fluorine binding site 3 out of 6 in the Crystal Structure of Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid


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 Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F125 b:32.2 occ:0.28 F2 A:BPD125 0.0 32.2 0.3 C1 A:BPD125 1.3 33.6 0.3 F1 A:BPD125 2.1 33.3 0.3 F3 A:BPD125 2.1 33.8 0.3 C2 A:BPD125 2.3 33.6 0.3 C3 A:BPD125 2.7 34.1 0.3 C7 A:BPD125 3.7 33.9 0.3 CB A:LEU110 3.7 16.0 1.0 CD2 A:LEU110 4.0 20.7 1.0 C4 A:BPD125 4.1 33.6 0.3 CG A:LEU110 4.4 20.0 1.0 N A:LEU110 4.7 16.7 1.0 CA A:LEU110 4.7 15.9 1.0 C6 A:BPD125 4.8 34.1 0.3 CD1 A:LEU110 4.9 20.1 1.0 CG2 A:THR119 5.0 26.2 1.0 C5 A:BPD125 5.0 34.3 0.3

Fluorine binding site 4 out of 6 in the Crystal Structure of Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid


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 Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F125 b:33.0 occ:0.28 F2 A:BPD125 0.0 33.0 0.3 C1 A:BPD125 1.3 34.0 0.3 F1 A:BPD125 2.1 33.3 0.3 F3 A:BPD125 2.1 33.6 0.3 C2 A:BPD125 2.3 33.5 0.3 C3 A:BPD125 2.7 34.6 0.3 C7 A:BPD125 3.7 33.9 0.3 CB B:LEU110 3.8 17.2 1.0 CD2 B:LEU110 4.1 22.7 1.0 C4 A:BPD125 4.1 33.7 0.3 CG B:LEU110 4.5 21.4 1.0 CG2 B:THR119 4.8 26.1 1.0 C6 A:BPD125 4.8 34.2 0.3 N B:LEU110 4.8 17.3 1.0 CA B:LEU110 4.8 17.5 1.0 C5 A:BPD125 5.0 34.5 0.3

Fluorine binding site 5 out of 6 in the Crystal Structure of Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid


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 Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F125 b:33.8 occ:0.28 F3 A:BPD125 0.0 33.8 0.3 C1 A:BPD125 1.3 33.6 0.3 F1 A:BPD125 2.1 33.3 0.3 F2 A:BPD125 2.1 32.2 0.3 C2 A:BPD125 2.3 33.6 0.3 C7 A:BPD125 2.9 33.9 0.3 CD1 A:LEU17 3.3 23.2 1.0 C3 A:BPD125 3.5 34.1 0.3 CB A:LEU110 3.5 16.0 1.0 CG A:LEU17 4.0 19.9 1.0 CD1 A:LEU110 4.0 20.1 1.0 CA A:LEU110 4.1 15.9 1.0 CG A:LEU110 4.2 20.0 1.0 O A:ALA109 4.2 17.6 1.0 CB A:LEU17 4.2 18.7 1.0 N A:LEU110 4.2 16.7 1.0 C6 A:BPD125 4.3 34.1 0.3 CD2 A:LEU110 4.3 20.7 1.0 C A:ALA109 4.3 18.1 1.0 C4 A:BPD125 4.6 33.6 0.3 C5 A:BPD125 5.0 34.3 0.3 CB A:ALA108 5.0 21.2 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid


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 Transthyretin in Complex with N-(M- Trifluoromethylphenyl) Phenoxazine-4,6-Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F125 b:33.6 occ:0.28 F3 A:BPD125 0.0 33.6 0.3 C1 A:BPD125 1.3 34.0 0.3 F1 A:BPD125 2.1 33.3 0.3 F2 A:BPD125 2.1 33.0 0.3 C2 A:BPD125 2.3 33.5 0.3 C7 A:BPD125 2.9 33.9 0.3 CD1 B:LEU17 3.3 23.4 1.0 C3 A:BPD125 3.5 34.6 0.3 CB B:LEU110 3.7 17.2 1.0 CG B:LEU17 4.0 23.7 1.0 CD1 B:LEU110 4.1 21.0 1.0 CA B:LEU110 4.2 17.5 1.0 C6 A:BPD125 4.3 34.2 0.3 CG B:LEU110 4.3 21.4 1.0 CB B:LEU17 4.3 20.2 1.0 O B:ALA109 4.3 19.9 1.0 N B:LEU110 4.3 17.3 1.0 CD2 B:LEU110 4.4 22.7 1.0 C B:ALA109 4.4 18.3 1.0 C4 A:BPD125 4.6 33.7 0.3 CB B:ALA108 4.9 21.6 1.0 C5 A:BPD125 5.0 34.5 0.3

T.Klabunde, H.M.Petrassi, V.B.Oza, P.Raman, J.W.Kelly, J.C.Sacchettini. Rational Design of Potent Human Transthyretin Amyloid Disease Inhibitors. Nat.Struct.Biol. V. 7 312 2000.
ISSN: ISSN 1072-8368
PubMed: 10742177
DOI: 10.1038/74082