Fluorine in PDB 5ody: Galectin-3C in Complex with Dithiogalactoside Derivative

The structure of Galectin-3C in Complex with Dithiogalactoside Derivative, PDB code: 5ody 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)	29.81 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.246, 57.443, 60.594, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 16.1

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

Fluorine binding site 1 out of 5 in the Galectin-3C in Complex with Dithiogalactoside Derivative


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 Dithiogalactoside Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:15.9 occ:1.00 F33 A:9SK301 0.0 15.9 1.0 C32 A:9SK301 1.3 13.5 1.0 C34 A:9SK301 2.3 12.3 1.0 C31 A:9SK301 2.4 12.5 1.0 H311 A:9SK301 2.5 15.0 1.0 F35 A:9SK301 2.7 14.1 1.0 O A:HOH501 3.1 21.3 1.0 HB2 A:SER237 3.3 14.9 1.0 OG A:SER237 3.5 12.0 1.0 NH2 A:ARG144 3.5 17.4 1.0 HH22 A:ARG144 3.6 20.9 1.0 C36 A:9SK301 3.6 11.4 1.0 C30 A:9SK301 3.6 11.2 1.0 CZ A:ARG144 3.7 14.8 1.0 HH21 A:ARG144 3.8 20.9 1.0 CB A:SER237 3.9 12.5 1.0 NH1 A:ARG144 4.0 17.1 1.0 HH12 A:ARG144 4.0 20.4 1.0 C38 A:9SK301 4.1 11.1 1.0 O A:HOH471 4.1 25.3 1.0 NE A:ARG144 4.2 13.6 1.0 HG A:SER237 4.3 14.3 1.0 HB3 A:SER237 4.3 14.9 1.0 O A:HOH520 4.4 21.9 1.0 HH11 A:ARG144 4.4 20.4 1.0 HE A:ARG144 4.4 16.3 1.0 F37 A:9SK301 4.6 12.2 1.0 HD2 A:ARG144 4.7 17.0 1.0 HA2 A:GLY238 4.8 11.3 1.0 C29 A:9SK301 4.8 11.1 1.0 HB3 A:ALA146 4.8 11.6 1.0 O A:HOH430 4.8 17.1 1.0 H A:GLY238 4.8 11.1 1.0 N A:GLY238 4.9 9.3 1.0

Fluorine binding site 2 out of 5 in the Galectin-3C in Complex with Dithiogalactoside Derivative


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 Dithiogalactoside Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:14.1 occ:1.00 F35 A:9SK301 0.0 14.1 1.0 C34 A:9SK301 1.3 12.3 1.0 C32 A:9SK301 2.4 13.5 1.0 C36 A:9SK301 2.4 11.4 1.0 HA2 A:GLY238 2.6 11.3 1.0 F33 A:9SK301 2.7 15.9 1.0 F37 A:9SK301 2.7 12.2 1.0 HA3 A:GLY238 3.0 11.3 1.0 HG3 A:ARG144 3.0 15.9 1.0 CA A:GLY238 3.1 9.4 1.0 N A:GLY238 3.1 9.3 1.0 HB2 A:SER237 3.2 14.9 1.0 OG A:SER237 3.2 12.0 1.0 H A:GLY238 3.4 11.1 1.0 C A:SER237 3.4 9.1 1.0 HE A:ARG144 3.4 16.3 1.0 NE A:ARG144 3.5 13.6 1.0 C31 A:9SK301 3.6 12.5 1.0 CB A:SER237 3.6 12.5 1.0 C38 A:9SK301 3.6 11.1 1.0 HD2 A:ARG144 3.7 17.0 1.0 O A:SER237 3.8 9.8 1.0 HB3 A:ALA146 3.8 11.6 1.0 CZ A:ARG144 3.9 14.8 1.0 CG A:ARG144 3.9 13.3 1.0 O A:HOH434 3.9 18.3 1.0 CD A:ARG144 3.9 14.2 1.0 HG A:SER237 3.9 14.3 1.0 H A:ALA146 4.1 10.0 1.0 C30 A:9SK301 4.1 11.2 1.0 HH21 A:ARG144 4.1 20.9 1.0 CA A:SER237 4.1 8.9 1.0 NH2 A:ARG144 4.2 17.4 1.0 HA A:ILE145 4.2 10.7 1.0 HB2 A:ALA146 4.2 11.6 1.0 O A:HOH540 4.4 30.1 1.0 N A:ALA146 4.4 8.3 1.0 HG2 A:ARG144 4.4 15.9 1.0 H311 A:9SK301 4.4 15.0 1.0 H381 A:9SK301 4.5 13.3 1.0 CB A:ALA146 4.5 9.7 1.0 HB3 A:SER237 4.5 14.9 1.0 NH1 A:ARG144 4.5 17.1 1.0 C A:GLY238 4.5 9.5 1.0 HB2 A:ARG144 4.6 13.3 1.0 HH11 A:ARG144 4.7 20.4 1.0 O A:ARG144 4.7 10.8 1.0 HA A:SER237 4.7 10.7 1.0 C A:ILE145 4.7 7.8 1.0 O A:HOH501 4.7 21.3 1.0 HH22 A:ARG144 4.7 20.9 1.0 HD3 A:ARG144 4.8 17.0 1.0 CA A:ILE145 4.8 9.0 1.0 O A:HOH526 4.8 16.1 1.0 CB A:ARG144 4.9 11.1 1.0 C A:ARG144 4.9 9.9 1.0 H A:ASP239 5.0 11.1 1.0

Fluorine binding site 3 out of 5 in the Galectin-3C in Complex with Dithiogalactoside Derivative


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 Dithiogalactoside Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:12.2 occ:1.00 F37 A:9SK301 0.0 12.2 1.0 C36 A:9SK301 1.3 11.4 1.0 C34 A:9SK301 2.3 12.3 1.0 C38 A:9SK301 2.3 11.1 1.0 H381 A:9SK301 2.5 13.3 1.0 HG3 A:ARG144 2.6 15.9 1.0 HB2 A:ARG144 2.6 13.3 1.0 F35 A:9SK301 2.7 14.1 1.0 HB2 A:ALA146 2.8 11.6 1.0 HD2 A:ARG144 2.9 17.0 1.0 C A:ILE145 3.1 7.8 1.0 CG A:ARG144 3.2 13.3 1.0 O A:ILE145 3.2 8.1 1.0 HD22 A:ASN160 3.2 10.3 1.0 HD21 A:ASN160 3.2 10.3 1.0 CB A:ARG144 3.3 11.1 1.0 N A:ALA146 3.3 8.3 1.0 N A:ILE145 3.3 9.4 1.0 CD A:ARG144 3.4 14.2 1.0 HB3 A:ALA146 3.5 11.6 1.0 CB A:ALA146 3.5 9.7 1.0 ND2 A:ASN160 3.5 8.6 1.0 H A:ILE145 3.5 11.3 1.0 HA A:ILE145 3.5 10.7 1.0 CA A:ILE145 3.5 9.0 1.0 C32 A:9SK301 3.6 13.5 1.0 H A:ALA146 3.6 10.0 1.0 C30 A:9SK301 3.6 11.2 1.0 C A:ARG144 3.6 9.9 1.0 CA A:ALA146 3.9 9.1 1.0 HA3 A:GLY238 3.9 11.3 1.0 CA A:ARG144 4.1 9.3 1.0 HB3 A:ARG144 4.1 13.3 1.0 HG2 A:ARG144 4.1 15.9 1.0 C31 A:9SK301 4.1 12.5 1.0 NE A:ARG144 4.1 13.6 1.0 O A:ARG144 4.1 10.8 1.0 HA A:ALA146 4.2 10.9 1.0 HD3 A:ARG144 4.3 17.0 1.0 HA2 A:GLY238 4.3 11.3 1.0 HB1 A:ALA146 4.3 11.6 1.0 HE A:ARG144 4.4 16.3 1.0 HA A:ARG144 4.4 11.1 1.0 O A:HOH537 4.5 14.2 1.0 O A:SER237 4.5 9.8 1.0 CA A:GLY238 4.5 9.4 1.0 HH11 A:ARG144 4.6 20.4 1.0 CG A:ASN160 4.6 8.0 1.0 F33 A:9SK301 4.6 15.9 1.0 OG A:SER237 4.7 12.0 1.0 C29 A:9SK301 4.8 11.1 1.0 CZ A:ARG144 4.8 14.8 1.0 O A:HOH522 4.8 30.9 1.0 C A:SER237 4.9 9.1 1.0 HA A:ASN160 4.9 8.3 1.0 H281 A:9SK301 4.9 13.2 1.0 NH1 A:ARG144 5.0 17.1 1.0 HG A:SER237 5.0 14.3 1.0 N A:GLY238 5.0 9.3 1.0

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


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 Dithiogalactoside Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:23.8 occ:1.00 F46 A:9SK301 0.0 23.8 1.0 C45 A:9SK301 1.3 23.0 1.0 C47 A:9SK301 2.3 24.7 1.0 C05 A:9SK301 2.4 20.8 1.0 H061 A:9SK301 2.6 21.5 1.0 F48 A:9SK301 2.7 27.1 1.0 HD3 A:ARG186 2.7 16.3 1.0 C06 A:9SK301 2.9 18.0 1.0 HH11 A:ARG186 2.9 15.1 1.0 NH1 A:ARG186 3.1 12.6 1.0 O A:HOH523 3.2 16.2 1.0 CZ A:ARG186 3.3 11.6 1.0 O A:HOH560 3.3 16.6 1.0 CD A:ARG186 3.3 13.6 1.0 NE A:ARG186 3.4 13.2 1.0 HD2 A:ARG186 3.4 16.3 1.0 HH12 A:ARG186 3.5 15.1 1.0 C49 A:9SK301 3.6 24.7 1.0 C04 A:9SK301 3.6 21.3 1.0 HE A:ARG186 3.9 15.8 1.0 C50 A:9SK301 4.1 23.2 1.0 NH2 A:ARG186 4.2 11.2 1.0 C07 A:9SK301 4.2 17.1 1.0 HH22 A:ARG186 4.5 13.4 1.0 H491 A:9SK301 4.5 29.6 1.0 HH21 A:ARG186 4.6 13.4 1.0 OE1 A:GLU165 4.7 14.6 1.0 CG A:ARG186 4.7 10.3 1.0 O03 A:9SK301 4.8 21.0 1.0 HG2 A:ARG186 5.0 12.4 1.0 C02 A:9SK301 5.0 20.4 1.0 HB2 A:ARG186 5.0 12.2 1.0

Fluorine binding site 5 out of 5 in the Galectin-3C in Complex with Dithiogalactoside Derivative


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 Dithiogalactoside Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:27.1 occ:1.00 F48 A:9SK301 0.0 27.1 1.0 C47 A:9SK301 1.3 24.7 1.0 C49 A:9SK301 2.3 24.7 1.0 C45 A:9SK301 2.4 23.0 1.0 H491 A:9SK301 2.6 29.6 1.0 F46 A:9SK301 2.7 23.8 1.0 O A:HOH560 3.3 16.6 1.0 C50 A:9SK301 3.6 23.2 1.0 C05 A:9SK301 3.6 20.8 1.0 O A:HOH523 3.8 16.2 1.0 O A:HOH531 4.1 27.3 1.0 C04 A:9SK301 4.1 21.3 1.0 O A:HOH505 4.2 23.7 1.0 H501 A:9SK301 4.4 27.8 1.0 O A:HOH552 4.4 14.6 1.0 HH11 A:ARG186 4.7 15.1 1.0 C06 A:9SK301 4.8 18.0 1.0 HD3 A:ARG186 4.9 16.3 1.0 H061 A:9SK301 5.0 21.5 1.0

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