Fluorine in PDB 5oax: Galectin-3C in Complex with Thiogalactoside Derivate

The structure of Galectin-3C in Complex with Thiogalactoside Derivate, PDB code: 5oax was solved by U.J.Nilsson, K.Peterson, M.Hakansson, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.07 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.190, 58.150, 62.810, 90.00, 90.00, 90.00
R / Rfree (%)	10.3 / 13.2

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

Fluorine binding site 1 out of 6 in the Galectin-3C in Complex with Thiogalactoside Derivate


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 Thiogalactoside Derivate within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:48.6 occ:0.50 F2 A:9Q5301 0.0 48.6 0.5 C28 A:9Q5301 1.3 30.3 0.5 C23 A:9Q5301 2.3 43.0 0.5 C27 A:9Q5301 2.4 33.1 0.5 O6 A:9Q5301 2.8 20.3 0.5 C17 A:9Q5301 2.8 19.7 0.5 C11 A:9Q5301 3.2 19.0 0.5 C24 A:9Q5301 3.6 44.4 0.5 C26 A:9Q5301 3.6 24.8 0.5 O A:HOH482 3.8 24.0 1.0 C13 A:9Q5301 4.0 16.8 0.5 C18 A:9Q5301 4.0 22.7 0.5 C25 A:9Q5301 4.1 36.8 0.5 CD A:ARG186 4.3 11.5 0.8 O9 A:9Q5301 4.3 21.9 0.5 C12 A:9Q5301 4.6 19.3 0.5 NE A:ARG186 4.9 10.2 0.7 C22 A:9Q5301 5.0 24.3 0.5

Fluorine binding site 2 out of 6 in the Galectin-3C in Complex with Thiogalactoside Derivate


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 Thiogalactoside Derivate within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:15.3 occ:0.50 F2 A:9Q5301 0.0 15.3 0.5 C28 A:9Q5301 1.3 13.3 0.5 CZ A:ARG144 1.8 12.7 0.5 NH1 A:ARG144 1.9 14.1 0.5 NE A:ARG144 2.2 11.1 0.5 C27 A:9Q5301 2.3 13.1 0.5 C23 A:9Q5301 2.3 15.3 0.5 NH2 A:ARG144 2.5 11.8 0.5 CD A:ARG144 2.8 13.5 0.5 CG A:ARG144 2.8 13.0 0.5 C A:ILE145 3.1 7.3 1.0 CG A:ARG144 3.3 15.7 0.5 CB A:ARG144 3.3 10.9 0.5 O A:ILE145 3.4 7.3 1.0 N A:ALA146 3.4 7.6 1.0 CB A:ARG144 3.4 10.7 0.5 CB A:ALA146 3.4 9.1 1.0 C26 A:9Q5301 3.5 13.0 0.5 N A:ILE145 3.6 8.8 1.0 C24 A:9Q5301 3.6 17.2 0.5 CA A:ILE145 3.7 8.8 1.0 C A:ARG144 3.7 9.8 1.0 CD A:ARG144 3.8 16.2 0.5 ND2 A:ASN160 3.8 8.6 1.0 CA A:ALA146 3.9 7.5 1.0 O A:HOH518 4.0 28.8 1.0 C25 A:9Q5301 4.1 16.0 0.5 CA A:ARG144 4.1 9.3 0.5 O A:ARG144 4.2 11.7 1.0 CA A:ARG144 4.2 8.6 0.5 CA A:GLY238 4.3 9.3 1.0 NE A:ARG144 4.3 18.1 0.5 O A:SER237 4.4 9.2 1.0 OG A:SER237 4.5 12.0 1.0 O A:HOH413 4.5 20.0 0.5 O A:HOH553 4.6 21.9 1.0 N A:GLY238 4.7 9.7 1.0 O A:HOH459 4.7 15.0 0.5 C A:SER237 4.7 8.6 1.0 C22 A:9Q5301 4.8 11.2 0.5 CG A:ASN160 4.9 8.0 1.0 CZ A:ARG144 4.9 22.2 0.5

Fluorine binding site 3 out of 6 in the Galectin-3C in Complex with Thiogalactoside Derivate


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 Thiogalactoside Derivate within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:23.7 occ:0.50 F1 A:9Q5301 0.0 23.7 0.5 C20 A:9Q5301 1.4 22.5 0.5 NH1 A:ARG144 1.6 29.5 0.5 C12 A:9Q5301 2.5 19.7 0.5 C19 A:9Q5301 2.5 20.0 0.5 F A:9Q5301 2.8 30.6 0.5 CZ A:ARG144 2.8 22.2 0.5 C15 A:9Q5301 2.9 19.9 0.5 CD A:ARG144 3.2 16.2 0.5 NE A:ARG144 3.3 11.1 0.5 NE A:ARG144 3.4 18.1 0.5 CD A:ARG144 3.5 13.5 0.5 C26 A:9Q5301 3.6 13.0 0.5 C22 A:9Q5301 3.7 11.2 0.5 C25 A:9Q5301 3.8 16.0 0.5 C11 A:9Q5301 3.8 17.6 0.5 C18 A:9Q5301 3.8 24.1 0.5 NH2 A:ARG144 3.9 27.1 0.5 CZ A:ARG144 3.9 12.7 0.5 O A:HOH553 3.9 21.9 1.0 C27 A:9Q5301 4.0 13.1 0.5 C21 A:9Q5301 4.0 12.4 0.5 O A:HOH459 4.1 15.0 0.5 C17 A:9Q5301 4.3 24.3 0.5 C A:9Q5301 4.3 19.5 0.5 NH2 A:ARG144 4.3 11.8 0.5 C24 A:9Q5301 4.4 17.2 0.5 N1 A:9Q5301 4.4 13.3 0.5 C28 A:9Q5301 4.5 13.3 0.5 NH1 A:ARG144 4.7 14.1 0.5 CG A:ARG144 4.7 15.7 0.5 C23 A:9Q5301 4.7 15.3 0.5 N A:9Q5301 4.8 11.1 0.5 O10 A:9Q5301 4.9 15.7 0.5 O A:HOH567 4.9 42.3 1.0 O6 A:9Q5301 4.9 22.9 0.5 CG A:ARG144 5.0 13.0 0.5

Fluorine binding site 4 out of 6 in the Galectin-3C in Complex with Thiogalactoside Derivate


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 Thiogalactoside Derivate within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:17.0 occ:0.50 F1 A:9Q5301 0.0 17.0 0.5 C20 A:9Q5301 1.3 21.0 0.5 C19 A:9Q5301 2.3 18.0 0.5 C12 A:9Q5301 2.4 19.3 0.5 N1 A:9Q5301 2.5 30.7 0.5 F A:9Q5301 2.6 23.2 0.5 C15 A:9Q5301 2.8 16.2 0.5 C25 A:9Q5301 3.0 36.8 0.5 C22 A:9Q5301 3.4 24.3 0.5 OE1 A:GLU165 3.5 15.8 1.0 N2 A:9Q5301 3.5 27.0 0.5 C26 A:9Q5301 3.6 24.8 0.5 C18 A:9Q5301 3.6 22.7 0.5 O A:HOH494 3.7 47.5 1.0 C11 A:9Q5301 3.7 19.0 0.5 CD A:GLU165 3.7 12.9 1.0 OE2 A:GLU165 3.9 14.4 1.0 NH1 A:ARG186 3.9 12.2 0.9 C24 A:9Q5301 3.9 44.4 0.5 NH2 A:ARG186 4.0 12.6 1.0 CZ A:ARG186 4.1 11.1 0.9 C17 A:9Q5301 4.1 19.7 0.5 C A:9Q5301 4.2 17.4 0.5 O A:HOH428 4.3 32.3 1.0 O A:HOH432 4.5 18.2 1.0 C21 A:9Q5301 4.5 18.0 0.5 CG A:GLU165 4.5 13.2 1.0 N A:9Q5301 4.6 17.0 0.5 OD1 A:ASN166 4.7 43.9 1.0 C27 A:9Q5301 4.8 33.1 0.5 O10 A:9Q5301 4.8 23.1 0.5 O6 A:9Q5301 4.8 20.3 0.5

Fluorine binding site 5 out of 6 in the Galectin-3C in Complex with Thiogalactoside Derivate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Galectin-3C in Complex with Thiogalactoside Derivate within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:30.6 occ:0.50 F A:9Q5301 0.0 30.6 0.5 CZ A:ARG144 0.9 22.2 0.5 NH2 A:ARG144 1.3 27.1 0.5 C19 A:9Q5301 1.4 20.0 0.5 NH1 A:ARG144 1.4 29.5 0.5 NE A:ARG144 2.0 18.1 0.5 C20 A:9Q5301 2.4 22.5 0.5 C18 A:9Q5301 2.4 24.1 0.5 F1 A:9Q5301 2.8 23.7 0.5 CD A:ARG144 3.1 16.2 0.5 CD A:ARG144 3.6 13.5 0.5 O A:HOH507 3.7 44.0 1.0 C17 A:9Q5301 3.7 24.3 0.5 C12 A:9Q5301 3.7 19.7 0.5 C24 A:9Q5301 3.9 17.2 0.5 O A:HOH518 4.0 28.8 1.0 C25 A:9Q5301 4.1 16.0 0.5 O A:HOH440 4.2 28.5 1.0 C11 A:9Q5301 4.2 17.6 0.5 NE A:ARG144 4.3 11.1 0.5 C23 A:9Q5301 4.4 15.3 0.5 CG A:ARG144 4.4 15.7 0.5 NH1 A:ARG144 4.6 14.1 0.5 CZ A:ARG144 4.7 12.7 0.5 C26 A:9Q5301 4.8 13.0 0.5 CG A:ARG144 4.8 13.0 0.5 C15 A:9Q5301 4.9 19.9 0.5 C28 A:9Q5301 5.0 13.3 0.5

Fluorine binding site 6 out of 6 in the Galectin-3C in Complex with Thiogalactoside Derivate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Galectin-3C in Complex with Thiogalactoside Derivate within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:23.2 occ:0.50 F A:9Q5301 0.0 23.2 0.5 C19 A:9Q5301 1.3 18.0 0.5 C20 A:9Q5301 2.3 21.0 0.5 C18 A:9Q5301 2.4 22.7 0.5 F1 A:9Q5301 2.6 17.0 0.5 O A:HOH494 2.7 47.5 1.0 C24 A:9Q5301 3.3 44.4 0.5 C25 A:9Q5301 3.4 36.8 0.5 O A:HOH605 3.4 20.6 0.6 O A:HOH432 3.5 18.2 1.0 C12 A:9Q5301 3.6 19.3 0.5 C17 A:9Q5301 3.7 19.7 0.5 OE1 A:GLU165 3.9 15.8 1.0 O A:HOH525 4.0 21.9 1.0 C11 A:9Q5301 4.1 19.0 0.5 NH1 A:ARG186 4.2 12.2 0.9 C23 A:9Q5301 4.4 43.0 0.5 O A:HOH605 4.4 15.1 0.5 C26 A:9Q5301 4.5 24.8 0.5 C15 A:9Q5301 4.7 16.2 0.5 N1 A:9Q5301 4.7 30.7 0.5 CD A:GLU165 4.8 12.9 1.0 CZ A:ARG186 5.0 11.1 0.9

K.Peterson, R.Kumar, O.Stenstrom, P.Verma, P.R.Verma, M.Hakansson, B.Kahl-Knutsson, F.Zetterberg, H.Leffler, M.Akke, D.T.Logan, U.J.Nilsson. Systematic Tuning of Fluoro-Galectin-3 Interactions Provides Thiodigalactoside Derivatives with Single-Digit Nm Affinity and High Selectivity. J. Med. Chem. V. 61 1164 2018.
ISSN: ISSN 1520-4804
PubMed: 29284090
DOI: 10.1021/ACS.JMEDCHEM.7B01626