Fluorine in PDB 7y28: Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1

All present enzymatic activity of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1:
6.1.1.15; 6.1.1.17;

The structure of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1, PDB code: 7y28 was solved by S.Kim, I.Yoon, J.Son, S.Park, K.Y.Hwang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.43 / 2.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.563, 92.38, 86.059, 90, 108.72, 90
R / Rfree (%)	20.7 / 26.4

The structure of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 (pdb code 7y28). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1, PDB code: 7y28:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2601 b:39.2 occ:1.00 F A:F962601 0.0 39.2 1.0 C17 A:F962601 1.4 36.4 1.0 C18 A:F962601 2.3 31.7 1.0 C16 A:F962601 2.3 25.1 1.0 NE2 A:HIS1093 2.8 39.4 1.0 CE1 A:HIS1093 3.0 50.2 1.0 CD2 A:HIS1093 3.4 46.0 1.0 CG2 A:VAL1101 3.5 36.7 1.0 C15 A:F962601 3.6 39.6 1.0 C13 A:F962601 3.6 32.6 1.0 ND1 A:HIS1093 3.7 43.2 1.0 CA A:ALA1098 3.9 35.7 1.0 CG A:HIS1093 3.9 46.8 1.0 C14 A:F962601 4.1 40.5 1.0 CB A:ALA1098 4.3 30.1 1.0 N A:ALA1098 4.4 40.1 1.0 O A:PHE1097 4.5 42.5 1.0 C A:PHE1097 4.6 42.3 1.0 CB A:VAL1101 4.7 35.1 1.0 CD1 A:LEU1087 4.8 41.6 1.0 O A:ALA1098 4.8 38.0 1.0 C12 A:F962601 4.8 32.6 1.0 C A:ALA1098 4.9 41.8 1.0

Fluorine binding site 2 out of 2 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2601 b:83.3 occ:1.00 F B:F962601 0.0 83.3 1.0 C17 B:F962601 1.4 58.4 1.0 C16 B:F962601 2.3 56.0 1.0 C18 B:F962601 2.3 44.7 1.0 O B:HOH2713 3.3 45.4 1.0 C15 B:F962601 3.6 55.7 1.0 C13 B:F962601 3.6 40.1 1.0 OG1 B:THR1092 3.7 92.8 1.0 CG2 B:THR1124 3.7 41.9 1.0 C14 B:F962601 4.1 47.0 1.0 OG1 B:THR1124 4.2 51.8 1.0 CG B:LEU1087 4.5 56.9 1.0 ND1 B:HIS1093 4.6 93.8 1.0 CB B:THR1124 4.6 41.9 1.0 O B:LEU1087 4.6 66.5 1.0 CG2 B:THR1092 4.7 93.5 1.0 CG2 B:THR1121 4.7 34.2 1.0 CB B:HIS1093 4.8 67.5 1.0 CB B:THR1092 4.8 86.2 1.0 C12 B:F962601 4.8 46.1 1.0 CG B:HIS1093 5.0 88.5 1.0

S.Kim, K.Hwang, I.Yoon. Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl-Trna Synthetase 1 To Be Published.