Fluorine in PDB 7df5: Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor

The structure of Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor, PDB code: 7df5 was solved by K.Ghosh, A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.30 / 1.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.21, 57.34, 62.06, 90, 90, 90
R / Rfree (%)	13.9 / 16.9

The structure of Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Fluorine atom in the Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor (pdb code 7df5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor, PDB code: 7df5:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F306 b:14.6 occ:1.00 F2 A:H5O306 0.0 14.6 1.0 C13 A:H5O306 1.3 13.6 1.0 C12 A:H5O306 2.3 15.8 1.0 C14 A:H5O306 2.4 13.2 1.0 H17 A:H5O306 2.6 13.7 1.0 F1 A:H5O306 2.6 18.1 1.0 HG3 A:ARG144 2.6 15.3 1.0 HB2 A:ARG144 2.7 14.2 1.0 HB2 A:ALA146 2.8 11.4 1.0 C A:ILE145 3.0 10.8 1.0 HD2 A:ARG144 3.2 16.8 1.0 O A:ILE145 3.3 10.9 1.0 CG A:ARG144 3.3 15.4 1.0 HD22 A:ASN160 3.3 11.9 0.0 N A:ILE145 3.3 11.1 1.0 N A:ALA146 3.3 10.5 1.0 CB A:ARG144 3.4 14.5 1.0 HD21 A:ASN160 3.4 11.9 0.0 HA A:ILE145 3.4 11.0 1.0 HB3 A:ALA146 3.4 11.7 1.0 CA A:ILE145 3.5 10.7 1.0 CB A:ALA146 3.5 11.8 1.0 H A:ILE145 3.5 11.2 1.0 C11 A:H5O306 3.5 18.3 1.0 ND2 A:ASN160 3.6 12.0 1.0 C A:ARG144 3.6 12.6 1.0 C9 A:H5O306 3.6 14.7 1.0 H A:ALA146 3.6 10.4 1.0 CD A:ARG144 3.7 15.9 1.0 HA3 A:GLY238 3.7 12.3 1.0 CA A:ALA146 3.9 10.0 1.0 O A:ARG144 4.1 12.8 1.0 CA A:ARG144 4.1 12.3 1.0 C10 A:H5O306 4.1 17.2 1.0 NE A:ARG144 4.1 20.7 1.0 HG2 A:ARG144 4.1 15.3 1.0 HB3 A:ARG144 4.2 13.9 1.0 HA2 A:GLY238 4.3 12.3 1.0 HA A:ALA146 4.3 10.1 1.0 HE A:ARG144 4.3 20.7 1.0 HB1 A:ALA146 4.3 11.4 1.0 CA A:GLY238 4.4 12.1 1.0 O A:SER237 4.4 11.7 1.0 HA A:ARG144 4.5 12.4 1.0 OG A:SER237 4.5 15.3 1.0 HD3 A:ARG144 4.5 16.5 1.0 F A:H5O306 4.6 23.2 1.0 HH21 A:ARG144 4.7 27.7 1.0 CZ A:ARG144 4.7 26.1 1.0 HG A:SER237 4.7 15.2 0.0 CG A:ASN160 4.8 11.0 1.0 C A:SER237 4.8 11.6 1.0 C8 A:H5O306 4.8 14.7 1.0 CL A:CL302 4.9 18.3 1.0 N A:GLY238 4.9 12.2 1.0 NH2 A:ARG144 4.9 28.9 1.0 H15 A:H5O306 4.9 13.6 1.0 CB A:ILE145 5.0 12.2 1.0

Fluorine binding site 2 out of 3 in the Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F306 b:18.1 occ:1.00 F1 A:H5O306 0.0 18.1 1.0 C12 A:H5O306 1.3 15.8 1.0 C13 A:H5O306 2.3 13.6 1.0 C11 A:H5O306 2.3 18.3 1.0 HA2 A:GLY238 2.6 12.3 1.0 F2 A:H5O306 2.6 14.6 1.0 F A:H5O306 2.7 23.2 1.0 HA3 A:GLY238 2.9 12.3 1.0 CA A:GLY238 3.0 12.1 1.0 N A:GLY238 3.1 12.2 1.0 HB2 A:SER237 3.1 14.2 1.0 HG3 A:ARG144 3.1 15.3 1.0 OG A:SER237 3.2 15.3 1.0 HG A:SER237 3.3 15.2 0.0 C A:SER237 3.4 11.6 1.0 HE A:ARG144 3.4 20.7 1.0 H A:GLY238 3.4 12.0 1.0 CB A:SER237 3.6 14.5 1.0 NE A:ARG144 3.6 20.7 1.0 C14 A:H5O306 3.6 13.2 1.0 C10 A:H5O306 3.6 17.2 1.0 O A:SER237 3.8 11.7 1.0 CZ A:ARG144 3.8 26.1 1.0 HH11 A:ARG144 3.9 30.3 1.0 HB3 A:ALA146 3.9 11.7 1.0 CG A:ARG144 4.0 15.4 1.0 HD2 A:ARG144 4.0 16.8 1.0 NH1 A:ARG144 4.0 32.0 1.0 CD A:ARG144 4.1 15.9 1.0 CA A:SER237 4.1 12.3 1.0 C9 A:H5O306 4.1 14.7 1.0 H A:ALA146 4.2 10.4 1.0 HA A:ILE145 4.2 11.0 1.0 O A:HOH524 4.3 17.5 1.0 O A:HOH505 4.3 31.1 1.0 HB2 A:ALA146 4.3 11.4 1.0 H17 A:H5O306 4.4 13.7 1.0 N A:ALA146 4.4 10.5 1.0 O A:HOH464 4.4 25.3 1.0 HB3 A:SER237 4.4 14.2 1.0 C A:GLY238 4.5 12.1 1.0 HG2 A:ARG144 4.5 15.3 1.0 H16 A:H5O306 4.5 16.7 1.0 HH12 A:ARG144 4.5 29.7 1.0 CB A:ALA146 4.6 11.8 1.0 NH2 A:ARG144 4.6 28.9 1.0 O A:HOH488 4.6 23.6 1.0 O A:ARG144 4.6 12.8 1.0 HB2 A:ARG144 4.7 14.2 1.0 HA A:SER237 4.7 12.3 1.0 C A:ILE145 4.7 10.8 1.0 CA A:ILE145 4.8 10.7 1.0 HH21 A:ARG144 4.8 27.7 1.0 C A:ARG144 4.9 12.6 1.0 CB A:ARG144 4.9 14.5 1.0 H A:ASP239 4.9 11.9 1.0 N A:ILE145 5.0 11.1 1.0

Fluorine binding site 3 out of 3 in the Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F306 b:23.2 occ:1.00 F A:H5O306 0.0 23.2 1.0 C11 A:H5O306 1.3 18.3 1.0 C12 A:H5O306 2.3 15.8 1.0 C10 A:H5O306 2.4 17.2 1.0 H16 A:H5O306 2.6 16.7 1.0 F1 A:H5O306 2.7 18.1 1.0 HG A:SER237 3.0 15.2 0.0 O A:HOH488 3.0 23.6 1.0 HB2 A:SER237 3.1 14.2 1.0 HH12 A:ARG144 3.4 29.7 1.0 NH1 A:ARG144 3.4 32.0 1.0 OG A:SER237 3.5 15.3 1.0 HH11 A:ARG144 3.5 30.3 1.0 C13 A:H5O306 3.5 13.6 1.0 C9 A:H5O306 3.6 14.7 1.0 CZ A:ARG144 3.8 26.1 1.0 CB A:SER237 3.8 14.5 1.0 O A:HOH471 3.8 45.2 1.0 C14 A:H5O306 4.0 13.2 1.0 HH22 A:ARG144 4.1 27.7 1.0 NH2 A:ARG144 4.1 28.9 1.0 HB3 A:SER237 4.2 14.2 1.0 NE A:ARG144 4.4 20.7 1.0 O A:HOH505 4.4 31.1 1.0 O A:HOH524 4.4 17.5 1.0 HE A:ARG144 4.5 20.7 1.0 F2 A:H5O306 4.6 14.6 1.0 HH21 A:ARG144 4.7 27.7 1.0 HA2 A:GLY238 4.7 12.3 1.0 H A:GLY238 4.7 12.0 1.0 C8 A:H5O306 4.8 14.7 1.0 N A:GLY238 4.8 12.2 1.0 HB3 A:ALA146 4.8 11.7 1.0 O A:HOH440 4.9 18.0 1.0

L.Xu, R.A.Hartz, B.R.Beno, K.Ghosh, J.K.Shukla, A.Kumar, D.Patel, N.Kalidindi, N.Lemos, S.S.Gautam, A.Kumar, B.A.Ellsworth, D.Shah, H.Sale, D.Cheng, A.Regueiro-Ren. Synthesis, Structure-Activity Relationships, and in Vivo Evaluation of Novel Tetrahydropyran-Based Thiodisaccharide Mimics As Galectin-3 Inhibitors. J.Med.Chem. V. 64 6634 2021.
ISSN: ISSN 0022-2623
PubMed: 33988358
DOI: 10.1021/ACS.JMEDCHEM.0C02001