Fluorine in PDB 6i76: Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative-3

The structure of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative-3, PDB code: 6i76 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)	31.49 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.833, 57.621, 62.978, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.3

The binding sites of Fluorine atom in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative-3 (pdb code 6i76). 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-3, PDB code: 6i76:
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-3


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-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:30.9 occ:1.00 F1 A:H5N301 0.0 30.9 1.0 C16 A:H5N301 1.3 29.5 1.0 C17 A:H5N301 2.3 31.7 1.0 C15 A:H5N301 2.3 26.9 1.0 N5 A:H5N301 2.7 26.8 1.0 F2 A:H5N301 2.7 34.7 1.0 C14 A:H5N301 2.8 26.0 1.0 HH12 A:ARG144 3.5 42.9 1.0 C20 A:H5N301 3.6 25.8 1.0 C18 A:H5N301 3.6 30.0 1.0 NH1 A:ARG144 3.8 35.8 1.0 N6 A:H5N301 3.9 25.8 1.0 HH11 A:ARG144 4.0 42.9 1.0 C19 A:H5N301 4.1 26.5 1.0 C13 A:H5N301 4.1 25.1 1.0 O A:HOH424 4.3 20.3 1.0 HH22 A:ARG144 4.5 46.0 1.0 CZ A:ARG144 4.5 36.5 1.0 O A:HOH408 4.5 34.6 1.0 N1 A:H5N301 4.6 24.1 1.0 F4 A:H5N301 4.7 27.5 1.0 NH2 A:ARG144 4.7 38.4 1.0 H14 A:H5N301 4.7 30.1 1.0 N2 A:H5N301 4.8 32.6 1.0

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


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-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:34.7 occ:1.00 F2 A:H5N301 0.0 34.7 1.0 C17 A:H5N301 1.3 31.7 1.0 C16 A:H5N301 2.3 29.5 1.0 C18 A:H5N301 2.4 30.0 1.0 N3 A:H5N301 2.6 33.9 1.0 F1 A:H5N301 2.7 30.9 1.0 N4 A:H5N301 2.7 35.0 1.0 N2 A:H5N301 2.9 32.6 1.0 O A:HOH450 3.4 48.7 1.0 NH2 A:ARG144 3.4 38.4 1.0 HH22 A:ARG144 3.4 46.0 1.0 CZ A:ARG144 3.5 36.5 1.0 C19 A:H5N301 3.6 26.5 1.0 C15 A:H5N301 3.6 26.9 1.0 HH21 A:ARG144 3.6 46.0 1.0 NH1 A:ARG144 3.8 35.8 1.0 HH12 A:ARG144 3.8 42.9 1.0 C20 A:H5N301 4.1 25.8 1.0 NE A:ARG144 4.1 33.8 1.0 HH11 A:ARG144 4.3 42.9 1.0 HE A:ARG144 4.3 40.5 1.0 HB3 A:SER237 4.4 20.5 0.5 HB2 A:SER237 4.4 16.8 0.5 HD2 A:ARG144 4.6 34.7 1.0 OG A:SER237 4.7 12.5 0.5 HB2 A:SER237 4.7 20.5 0.5 F3 A:H5N301 4.7 26.1 1.0 C14 A:H5N301 4.8 26.0 1.0 CD A:ARG144 5.0 28.9 1.0 CB A:SER237 5.0 17.1 0.5

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


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-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:26.1 occ:1.00 F3 A:H5N301 0.0 26.1 1.0 C19 A:H5N301 1.3 26.5 1.0 C20 A:H5N301 2.3 25.8 1.0 C18 A:H5N301 2.4 30.0 1.0 HG3 A:ARG144 2.6 27.5 1.0 HB2 A:ALA146 2.6 16.1 1.0 F4 A:H5N301 2.7 27.5 1.0 N2 A:H5N301 2.8 32.6 1.0 HD2 A:ARG144 2.9 34.7 1.0 HB2 A:ARG144 3.0 22.4 1.0 CG A:ARG144 3.3 23.0 1.0 HB3 A:ALA146 3.3 16.1 1.0 CB A:ALA146 3.3 13.4 1.0 C A:ILE145 3.3 11.6 1.0 N A:ALA146 3.4 12.1 1.0 CD A:ARG144 3.5 28.9 1.0 O A:ILE145 3.5 12.1 1.0 CB A:ARG144 3.6 18.7 1.0 C17 A:H5N301 3.6 31.7 1.0 H A:ALA146 3.6 14.4 1.0 C15 A:H5N301 3.6 26.9 1.0 HD21 A:ASN160 3.7 16.5 1.0 HD22 A:ASN160 3.7 16.5 1.0 HA A:ILE145 3.7 15.3 1.0 N A:ILE145 3.8 13.6 1.0 HA3 A:GLY238 3.8 19.0 1.0 CA A:ILE145 3.8 12.8 1.0 ND2 A:ASN160 3.9 13.7 1.0 CA A:ALA146 3.9 11.9 1.0 C A:ARG144 3.9 16.0 1.0 N3 A:H5N301 4.0 33.9 1.0 H A:ILE145 4.0 16.3 1.0 HA2 A:GLY238 4.1 19.0 1.0 C16 A:H5N301 4.1 29.5 1.0 HB1 A:ALA146 4.1 16.1 1.0 HG2 A:ARG144 4.1 27.5 1.0 NE A:ARG144 4.2 33.8 1.0 OG A:SER237 4.2 12.5 0.5 HB2 A:SER237 4.2 20.5 0.5 O A:ARG144 4.3 17.8 1.0 HA A:ALA146 4.3 14.2 1.0 HD3 A:ARG144 4.3 34.7 1.0 HB3 A:ARG144 4.3 22.4 1.0 CA A:GLY238 4.4 15.8 1.0 HE A:ARG144 4.4 40.5 1.0 CA A:ARG144 4.4 15.4 1.0 O A:SER237 4.4 14.1 1.0 O A:HOH494 4.4 31.2 1.0 HG A:SER237 4.5 15.0 0.5 C A:SER237 4.7 14.3 1.0 HH11 A:ARG144 4.7 42.9 1.0 N A:GLY238 4.7 14.8 1.0 F2 A:H5N301 4.7 34.7 1.0 C14 A:H5N301 4.8 26.0 1.0 CZ A:ARG144 4.9 36.5 1.0 HA A:ARG144 4.9 18.5 1.0 O A:HOH424 4.9 20.3 1.0 CG A:ASN160 4.9 13.7 1.0 O A:HOH408 5.0 34.6 1.0

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


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-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:27.5 occ:1.00 F4 A:H5N301 0.0 27.5 1.0 C20 A:H5N301 1.3 25.8 1.0 C15 A:H5N301 2.3 26.9 1.0 C19 A:H5N301 2.4 26.5 1.0 H14 A:H5N301 2.5 30.1 1.0 HB2 A:ALA146 2.6 16.1 1.0 F3 A:H5N301 2.7 26.1 1.0 C14 A:H5N301 2.8 26.0 1.0 C13 A:H5N301 2.8 25.1 1.0 HD21 A:ASN160 3.0 16.5 1.0 HE1 A:HIS158 3.0 15.8 1.0 ND2 A:ASN160 3.1 13.7 1.0 O A:HOH494 3.3 31.2 1.0 HD22 A:ASN160 3.4 16.5 1.0 CG A:ASN160 3.4 13.7 1.0 HE2 A:HIS158 3.5 15.8 1.0 CB A:ALA146 3.5 13.4 1.0 HD2 A:ARG144 3.6 34.7 1.0 C16 A:H5N301 3.6 29.5 1.0 C18 A:H5N301 3.6 30.0 1.0 OD1 A:ASN160 3.6 14.9 1.0 CE1 A:HIS158 3.7 13.2 1.0 HB1 A:ALA146 3.8 16.1 1.0 O A:HOH424 3.8 20.3 1.0 HB3 A:ALA146 3.9 16.1 1.0 O A:HOH408 3.9 34.6 1.0 NE2 A:HIS158 3.9 13.2 1.0 HB2 A:ASN160 4.0 15.4 1.0 HB2 A:ARG144 4.0 22.4 1.0 N5 A:H5N301 4.1 26.8 1.0 N1 A:H5N301 4.1 24.1 1.0 C17 A:H5N301 4.1 31.7 1.0 CB A:ASN160 4.3 12.9 1.0 O3 A:H5N301 4.3 18.4 1.0 O A:ILE145 4.4 12.1 1.0 HH11 A:ARG144 4.5 42.9 1.0 CD A:ARG144 4.5 28.9 1.0 CA A:ALA146 4.6 11.9 1.0 H17 A:H5N301 4.7 22.1 1.0 N6 A:H5N301 4.7 25.8 1.0 HG3 A:ARG144 4.7 27.5 1.0 F1 A:H5N301 4.7 30.9 1.0 HA A:ALA146 4.7 14.2 1.0 HA A:ASN160 4.8 12.2 1.0 N2 A:H5N301 4.8 32.6 1.0 C A:ILE145 4.8 11.6 1.0 CB A:ARG144 4.9 18.7 1.0 ND1 A:HIS158 4.9 11.6 1.0 N A:ALA146 4.9 12.1 1.0 CG A:ARG144 4.9 23.0 1.0 HD3 A:ARG144 5.0 34.7 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