Fluorine in PDB 6i78: Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5

The structure of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5, PDB code: 6i78 was solved by R.Kumar, K.Peterson, U.J.Nilsson, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.45 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.307, 57.628, 62.913, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 16.8

The binding sites of Fluorine atom in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5 (pdb code 6i78). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5, PDB code: 6i78:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:35.8 occ:1.00 F05 A:H5H301 0.0 35.8 1.0 C04 A:H5H301 1.3 31.4 1.0 C06 A:H5H301 2.3 30.0 1.0 C03 A:H5H301 2.4 27.8 1.0 F07 A:H5H301 2.7 34.8 1.0 H021 A:H5H301 2.7 34.8 1.0 N02 A:H5H301 2.9 29.0 1.0 O A:HOH404 3.4 32.8 1.0 HH21 A:ARG144 3.5 40.6 1.0 NH2 A:ARG144 3.5 33.8 1.0 HH22 A:ARG144 3.6 40.6 1.0 C34 A:H5H301 3.6 23.8 1.0 C08 A:H5H301 3.6 24.2 1.0 H011 A:H5H301 3.7 33.4 1.0 C01 A:H5H301 3.8 27.8 1.0 CZ A:ARG144 4.0 33.0 1.0 C32 A:H5H301 4.1 21.5 1.0 H013 A:H5H301 4.4 33.4 1.0 HE A:ARG144 4.5 37.0 1.0 NE A:ARG144 4.5 30.8 1.0 NH1 A:ARG144 4.6 33.0 1.0 HH12 A:ARG144 4.6 39.6 1.0 H012 A:H5H301 4.7 33.4 1.0 F35 A:H5H301 4.7 26.8 1.0 C09 A:H5H301 4.8 21.6 1.0

Fluorine binding site 2 out of 4 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:34.8 occ:1.00 F07 A:H5H301 0.0 34.8 1.0 C06 A:H5H301 1.3 30.0 1.0 C08 A:H5H301 2.3 24.2 1.0 C04 A:H5H301 2.3 31.4 1.0 F05 A:H5H301 2.7 35.8 1.0 N31 A:H5H301 2.8 21.6 1.0 C09 A:H5H301 2.8 21.6 1.0 O A:HOH471 3.4 38.8 1.0 C32 A:H5H301 3.6 21.5 1.0 C03 A:H5H301 3.6 27.8 1.0 HH12 A:ARG144 3.7 39.6 1.0 HH22 A:ARG144 3.7 40.6 1.0 N30 A:H5H301 4.0 19.5 1.0 C34 A:H5H301 4.1 23.8 1.0 C10 A:H5H301 4.1 19.6 1.0 NH1 A:ARG144 4.1 33.0 1.0 NH2 A:ARG144 4.1 33.8 1.0 O A:HOH404 4.2 32.8 1.0 CZ A:ARG144 4.3 33.0 1.0 O A:HOH454 4.5 16.4 1.0 HH11 A:ARG144 4.6 39.6 1.0 N11 A:H5H301 4.6 17.8 1.0 HH21 A:ARG144 4.6 40.6 1.0 F33 A:H5H301 4.7 20.8 1.0 H101 A:H5H301 4.8 23.6 1.0 N02 A:H5H301 4.9 29.0 1.0 H021 A:H5H301 5.0 34.8 1.0

Fluorine binding site 3 out of 4 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:20.8 occ:1.00 F33 A:H5H301 0.0 20.8 1.0 C32 A:H5H301 1.3 21.5 1.0 C34 A:H5H301 2.3 23.8 1.0 C08 A:H5H301 2.3 24.2 1.0 F35 A:H5H301 2.6 26.8 1.0 H101 A:H5H301 2.7 23.6 1.0 C09 A:H5H301 2.8 21.6 1.0 HB2 A:ALA146 2.8 12.1 1.0 C10 A:H5H301 2.9 19.6 1.0 HE1 A:HIS158 3.0 10.6 1.0 HD2 A:ARG144 3.1 30.1 1.0 HD21 A:ASN160 3.1 11.9 1.0 ND2 A:ASN160 3.3 9.9 1.0 O A:HOH507 3.4 30.3 1.0 HH11 A:ARG144 3.4 39.6 1.0 C06 A:H5H301 3.6 30.0 1.0 HD22 A:ASN160 3.6 11.9 1.0 O A:HOH454 3.6 16.4 1.0 CG A:ASN160 3.6 9.2 1.0 C03 A:H5H301 3.6 27.8 1.0 CB A:ALA146 3.7 10.1 1.0 CE1 A:HIS158 3.7 8.9 1.0 H141 A:H5H301 3.7 17.7 1.0 OD1 A:ASN160 3.8 11.2 1.0 HB1 A:ALA146 3.9 12.1 1.0 NH1 A:ARG144 3.9 33.0 1.0 NE2 A:HIS158 4.0 10.1 1.0 HB3 A:ALA146 4.0 12.1 1.0 N31 A:H5H301 4.0 21.6 1.0 C04 A:H5H301 4.0 31.4 1.0 CD A:ARG144 4.1 25.1 1.0 N11 A:H5H301 4.1 17.8 1.0 HB2 A:ASN160 4.2 10.8 1.0 HH12 A:ARG144 4.3 39.6 1.0 HB2 A:ARG144 4.3 17.6 1.0 O14 A:H5H301 4.3 14.8 1.0 HD3 A:ARG144 4.5 30.1 1.0 CB A:ASN160 4.5 9.0 1.0 O A:HOH404 4.5 32.8 1.0 CZ A:ARG144 4.5 33.0 1.0 NE A:ARG144 4.6 30.8 1.0 F07 A:H5H301 4.7 34.8 1.0 N30 A:H5H301 4.7 19.5 1.0 O A:ILE145 4.7 8.2 1.0 HG3 A:ARG144 4.7 25.3 1.0 N02 A:H5H301 4.8 29.0 1.0 CA A:ALA146 4.9 8.5 1.0 CG A:ARG144 4.9 21.0 1.0 ND1 A:HIS158 4.9 8.6 1.0 HA A:ALA146 4.9 10.2 1.0

Fluorine binding site 4 out of 4 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:26.8 occ:1.00 F35 A:H5H301 0.0 26.8 1.0 C34 A:H5H301 1.3 23.8 1.0 C32 A:H5H301 2.3 21.5 1.0 C03 A:H5H301 2.4 27.8 1.0 HD2 A:ARG144 2.4 30.1 1.0 HG3 A:ARG144 2.6 25.3 1.0 F33 A:H5H301 2.6 20.8 1.0 HB2 A:ALA146 2.8 12.1 1.0 N02 A:H5H301 2.8 29.0 1.0 H012 A:H5H301 3.1 33.4 1.0 CD A:ARG144 3.1 25.1 1.0 HB2 A:ARG144 3.2 17.6 1.0 CG A:ARG144 3.2 21.0 1.0 C01 A:H5H301 3.4 27.8 1.0 HB3 A:ALA146 3.4 12.1 1.0 CB A:ALA146 3.5 10.1 1.0 C04 A:H5H301 3.6 31.4 1.0 NE A:ARG144 3.6 30.8 1.0 C08 A:H5H301 3.6 24.2 1.0 H021 A:H5H301 3.7 34.8 1.0 CB A:ARG144 3.7 14.7 1.0 HD21 A:ASN160 3.7 11.9 1.0 C A:ILE145 3.8 7.9 1.0 HE A:ARG144 3.9 37.0 1.0 N A:ALA146 3.9 9.0 1.0 HD3 A:ARG144 3.9 30.1 1.0 HD22 A:ASN160 4.0 11.9 1.0 H011 A:H5H301 4.0 33.4 1.0 O A:HOH404 4.0 32.8 1.0 O A:ILE145 4.0 8.2 1.0 C06 A:H5H301 4.0 30.0 1.0 ND2 A:ASN160 4.1 9.9 1.0 HG2 A:ARG144 4.1 25.3 1.0 HH11 A:ARG144 4.1 39.6 1.0 H A:ALA146 4.2 10.8 1.0 CZ A:ARG144 4.2 33.0 1.0 HA3 A:GLY238 4.2 12.5 1.0 HB1 A:ALA146 4.3 12.1 1.0 N A:ILE145 4.3 9.8 1.0 HA2 A:GLY238 4.3 12.5 1.0 HB2 A:SER237 4.3 14.5 0.4 HA A:ILE145 4.3 11.4 1.0 OG A:SER237 4.3 10.5 0.6 CA A:ALA146 4.3 8.5 1.0 H013 A:H5H301 4.3 33.4 1.0 NH1 A:ARG144 4.4 33.0 1.0 C A:ARG144 4.4 10.5 1.0 CA A:ILE145 4.4 9.5 1.0 HB3 A:ARG144 4.4 17.6 1.0 H A:ILE145 4.5 11.8 1.0 CA A:GLY238 4.6 10.4 1.0 O A:ARG144 4.6 12.3 0.9 O A:HOH454 4.7 16.4 1.0 HG A:SER237 4.7 12.6 0.6 O A:HOH507 4.7 30.3 1.0 F05 A:H5H301 4.7 35.8 1.0 CA A:ARG144 4.7 10.2 1.0 HA A:ALA146 4.7 10.2 1.0 C09 A:H5H301 4.8 21.6 1.0 O A:SER237 4.8 10.4 1.0 N A:GLY238 4.9 10.7 1.0 C A:SER237 5.0 9.8 1.0 HB3 A:SER237 5.0 14.5 0.4 HH12 A:ARG144 5.0 39.6 1.0

R.Kumar, K.Peterson, M.Misini Ignjatovic, H.Leffler, U.Ryde, U.J.Nilsson, D.T.Logan. Substituted Polyfluoroaryl Interactions with An Arginine Side Chain in Galectin-3 Are Governed By Steric-, Desolvation and Electronic Conjugation Effects. Org. Biomol. Chem. V. 17 1081 2019.
ISSN: ESSN 1477-0539
PubMed: 30632578
DOI: 10.1039/C8OB02888E