Fluorine in PDB 7df6: Mouse Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor

The structure of Mouse Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor, PDB code: 7df6 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)	22.65 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.14, 58.14, 130.06, 90, 90, 90
R / Rfree (%)	19 / 25.5

The binding sites of Fluorine atom in the Mouse Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor (pdb code 7df6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Mouse Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor, PDB code: 7df6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Mouse 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 Mouse Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:24.8 occ:1.00 F2 A:H5O301 0.0 24.8 1.0 C13 A:H5O301 1.3 21.3 1.0 C12 A:H5O301 2.3 23.9 1.0 C14 A:H5O301 2.4 15.4 1.0 F1 A:H5O301 2.5 43.4 1.0 H17 A:H5O301 2.7 14.7 1.0 HD3 A:ARG158 2.8 19.7 1.0 HG3 A:ARG158 2.8 15.3 1.0 NE A:ARG158 3.1 21.9 1.0 HE A:ARG158 3.2 22.4 1.0 H10 B:H5O301 3.2 15.9 1.0 CD A:ARG158 3.2 19.7 1.0 H8 B:H5O301 3.3 16.2 1.0 CG A:ARG158 3.4 14.9 1.0 C11 A:H5O301 3.5 24.2 1.0 H17 B:H5O301 3.5 17.1 1.0 C9 A:H5O301 3.5 11.6 1.0 CZ A:ARG158 3.6 26.5 1.0 HG2 A:ARG158 3.7 15.5 1.0 C B:H5O301 3.8 16.2 1.0 C10 A:H5O301 3.9 15.0 1.0 C14 B:H5O301 4.0 18.4 1.0 HG22 A:VAL160 4.0 13.7 1.0 HG23 A:VAL160 4.0 13.2 1.0 NH2 A:ARG158 4.1 28.4 1.0 HH21 A:ARG158 4.1 26.9 1.0 NH1 A:ARG158 4.2 29.9 1.0 HD2 A:ARG158 4.2 18.5 1.0 HH11 A:ARG158 4.2 28.1 1.0 H9 B:H5O301 4.3 16.1 1.0 C9 B:H5O301 4.4 13.0 1.0 HA2 A:GLY252 4.5 10.4 1.0 C8 B:H5O301 4.5 13.2 1.0 H15 B:H5O301 4.5 11.1 1.0 CG2 A:VAL160 4.5 14.2 1.0 C7 B:H5O301 4.5 11.2 1.0 F A:H5O301 4.6 31.9 1.0 O A:HOH473 4.6 13.7 1.0 C13 B:H5O301 4.7 22.7 1.0 HH22 A:ARG158 4.7 27.6 1.0 HH12 A:ARG158 4.8 29.6 1.0 CB A:ARG158 4.8 13.2 1.0 C8 A:H5O301 4.8 15.6 1.0 O B:H5O301 4.8 15.3 1.0 HB3 A:ARG158 4.9 13.0 1.0 F2 B:H5O301 4.9 25.8 1.0

Fluorine binding site 2 out of 6 in the Mouse 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 Mouse Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:43.4 occ:1.00 F1 A:H5O301 0.0 43.4 1.0 C12 A:H5O301 1.2 23.9 1.0 C11 A:H5O301 2.2 24.2 1.0 C13 A:H5O301 2.2 21.3 1.0 F2 A:H5O301 2.5 24.8 1.0 F A:H5O301 2.6 31.9 1.0 H8 B:H5O301 2.8 16.2 1.0 H10 B:H5O301 3.1 15.9 1.0 C B:H5O301 3.3 16.2 1.0 C10 A:H5O301 3.4 15.0 1.0 HB3 A:SER251 3.5 15.4 1.0 C14 A:H5O301 3.5 15.4 1.0 O B:H5O301 3.7 15.3 1.0 HB2 A:SER251 3.7 15.7 1.0 C8 B:H5O301 3.7 13.2 1.0 N1 B:H5O301 3.8 15.2 1.0 N2 B:H5O301 3.9 15.2 1.0 C7 B:H5O301 3.9 11.2 1.0 HA2 A:GLY252 3.9 10.4 1.0 C9 A:H5O301 3.9 11.6 1.0 N B:H5O301 3.9 11.3 1.0 CB A:SER251 4.0 15.6 1.0 HD3 A:ARG158 4.1 19.7 1.0 HG22 A:VAL160 4.1 13.7 1.0 H A:GLY252 4.2 10.2 1.0 O B:HOH453 4.3 17.4 1.0 C9 B:H5O301 4.3 13.0 1.0 O A:HOH458 4.3 22.5 1.0 H16 A:H5O301 4.3 14.9 1.0 HG23 A:VAL160 4.3 13.2 1.0 H9 B:H5O301 4.3 16.1 1.0 N A:GLY252 4.4 9.9 1.0 H17 A:H5O301 4.4 14.7 1.0 H17 B:H5O301 4.4 17.1 1.0 H15 B:H5O301 4.4 11.1 1.0 HG A:SER251 4.4 11.8 0.0 CA A:GLY252 4.6 10.6 1.0 C14 B:H5O301 4.6 18.4 1.0 C6 B:H5O301 4.6 10.2 1.0 H4 B:H5O301 4.6 10.5 1.0 C1 B:H5O301 4.6 11.6 1.0 CG2 A:VAL160 4.7 14.2 1.0 HB A:VAL160 4.7 11.8 1.0 HG3 A:ARG158 4.7 15.3 1.0 HA3 A:GLY252 4.8 10.8 1.0 OG A:SER251 4.8 20.4 1.0 CD A:ARG158 4.9 19.7 1.0 HG2 A:ARG158 4.9 15.5 1.0 H B:H5O301 4.9 11.6 1.0 C A:SER251 4.9 11.8 1.0

Fluorine binding site 3 out of 6 in the Mouse 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 Mouse Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:31.9 occ:1.00 F A:H5O301 0.0 31.9 1.0 C11 A:H5O301 1.4 24.2 1.0 C12 A:H5O301 2.3 23.9 1.0 C10 A:H5O301 2.4 15.0 1.0 F1 A:H5O301 2.6 43.4 1.0 H16 A:H5O301 2.6 14.9 1.0 HG A:SER251 2.9 11.8 0.0 HB2 A:SER251 3.4 15.7 1.0 O A:HOH442 3.4 27.3 1.0 N1 B:H5O301 3.5 15.2 1.0 HB3 A:SER251 3.5 15.4 1.0 O B:HOH409 3.5 45.5 1.0 C13 A:H5O301 3.6 21.3 1.0 OG A:SER251 3.7 20.4 1.0 C9 A:H5O301 3.7 11.6 1.0 CB A:SER251 3.7 15.6 1.0 N2 B:H5O301 4.0 15.2 1.0 C8 B:H5O301 4.1 13.2 1.0 O B:HOH453 4.1 17.4 1.0 C14 A:H5O301 4.1 15.4 1.0 H16 B:H5O301 4.1 16.6 1.0 HG22 A:VAL160 4.2 13.7 1.0 HB A:VAL160 4.4 11.8 1.0 C9 B:H5O301 4.4 13.0 1.0 C10 B:H5O301 4.4 16.5 1.0 HG12 A:VAL160 4.5 12.8 1.0 F2 A:H5O301 4.6 24.8 1.0 O A:HOH422 4.7 20.9 1.0 N B:H5O301 4.8 11.3 1.0 CG2 A:VAL160 4.9 14.2 1.0 C8 A:H5O301 4.9 15.6 1.0 C7 B:H5O301 4.9 11.2 1.0 CB A:VAL160 5.0 11.4 1.0

Fluorine binding site 4 out of 6 in the Mouse 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 4 of Mouse Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:25.8 occ:1.00 F2 B:H5O301 0.0 25.8 1.0 C13 B:H5O301 1.3 22.7 1.0 C12 B:H5O301 2.3 24.9 1.0 C14 B:H5O301 2.3 18.4 1.0 F1 B:H5O301 2.6 44.2 1.0 H17 B:H5O301 2.6 17.1 1.0 HD3 B:ARG158 2.8 21.5 1.0 HG3 B:ARG158 2.8 17.2 1.0 H8 A:H5O301 3.0 16.0 1.0 NE B:ARG158 3.1 23.6 1.0 CD B:ARG158 3.2 20.6 1.0 HE B:ARG158 3.2 23.5 1.0 CG B:ARG158 3.4 17.2 1.0 H9 A:H5O301 3.5 17.3 1.0 C11 B:H5O301 3.5 25.2 1.0 C9 B:H5O301 3.5 13.0 1.0 CZ B:ARG158 3.6 27.8 1.0 HG2 B:ARG158 3.6 17.9 1.0 C A:H5O301 3.7 17.1 1.0 H17 A:H5O301 3.7 14.7 1.0 C10 B:H5O301 4.0 16.5 1.0 HG23 B:VAL160 4.0 12.4 1.0 HG22 B:VAL160 4.0 11.9 1.0 HH21 B:ARG158 4.1 31.4 1.0 NH2 B:ARG158 4.1 34.0 1.0 C14 A:H5O301 4.1 15.4 1.0 HD2 B:ARG158 4.1 19.2 1.0 NH1 B:ARG158 4.2 31.5 1.0 H10 A:H5O301 4.2 17.0 1.0 HH11 B:ARG158 4.3 30.4 1.0 CG2 B:VAL160 4.5 12.5 1.0 C8 A:H5O301 4.5 15.6 1.0 C9 A:H5O301 4.5 11.6 1.0 F B:H5O301 4.5 35.7 1.0 HA2 B:GLY252 4.5 12.1 1.0 C7 A:H5O301 4.6 10.6 1.0 O B:HOH465 4.6 20.3 1.0 H15 A:H5O301 4.6 11.4 1.0 C13 A:H5O301 4.7 21.3 1.0 HH22 B:ARG158 4.7 31.9 1.0 C8 B:H5O301 4.7 13.2 1.0 CB B:ARG158 4.8 14.5 1.0 HH12 B:ARG158 4.8 29.7 1.0 O A:H5O301 4.9 16.6 1.0 F2 A:H5O301 4.9 24.8 1.0 HB3 B:ARG158 4.9 14.0 1.0 HG21 B:VAL160 4.9 12.3 1.0

Fluorine binding site 5 out of 6 in the Mouse 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 5 of Mouse Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:44.2 occ:1.00 F1 B:H5O301 0.0 44.2 1.0 C12 B:H5O301 1.3 24.9 1.0 C11 B:H5O301 2.3 25.2 1.0 C13 B:H5O301 2.3 22.7 1.0 F2 B:H5O301 2.6 25.8 1.0 F B:H5O301 2.6 35.7 1.0 H8 A:H5O301 2.9 16.0 1.0 H9 A:H5O301 3.0 17.3 1.0 HB3 B:SER251 3.2 15.1 1.0 C A:H5O301 3.4 17.1 1.0 HB2 B:SER251 3.5 15.0 1.0 C10 B:H5O301 3.5 16.5 1.0 C14 B:H5O301 3.6 18.4 1.0 HA2 B:GLY252 3.8 12.1 1.0 N1 A:H5O301 3.8 19.7 1.0 CB B:SER251 3.8 14.9 1.0 O A:H5O301 3.9 16.6 1.0 N2 A:H5O301 3.9 19.1 1.0 HD3 B:ARG158 3.9 21.5 1.0 H B:GLY252 4.0 11.1 1.0 HG22 B:VAL160 4.0 11.9 1.0 C8 A:H5O301 4.0 15.6 1.0 HG23 B:VAL160 4.0 12.4 1.0 C9 B:H5O301 4.0 13.0 1.0 N A:H5O301 4.1 13.3 1.0 N B:GLY252 4.2 11.5 1.0 C7 A:H5O301 4.2 10.6 1.0 O B:HOH442 4.3 25.0 1.0 O A:HOH443 4.3 16.4 1.0 HG B:SER251 4.3 11.8 0.0 H10 A:H5O301 4.4 17.0 1.0 CA B:GLY252 4.4 11.9 1.0 H16 B:H5O301 4.4 16.6 1.0 HB B:VAL160 4.4 11.4 1.0 CG2 B:VAL160 4.4 12.5 1.0 H17 B:H5O301 4.5 17.1 1.0 C9 A:H5O301 4.6 11.6 1.0 HA3 B:GLY252 4.7 12.0 1.0 OG B:SER251 4.7 20.1 1.0 HG3 B:ARG158 4.7 17.2 1.0 HG2 B:ARG158 4.7 17.9 1.0 C B:SER251 4.7 10.5 1.0 CD B:ARG158 4.8 20.6 1.0 H15 A:H5O301 4.8 11.4 1.0 H17 A:H5O301 4.8 14.7 1.0 H4 A:H5O301 4.8 11.0 1.0 C6 A:H5O301 4.9 10.8 1.0 C1 A:H5O301 4.9 12.7 1.0 O B:HOH405 4.9 22.4 1.0 C14 A:H5O301 4.9 15.4 1.0 CA B:SER251 5.0 11.8 1.0 CG B:ARG158 5.0 17.2 1.0

Fluorine binding site 6 out of 6 in the Mouse 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 6 of Mouse Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:35.7 occ:1.00 F B:H5O301 0.0 35.7 1.0 C11 B:H5O301 1.3 25.2 1.0 C12 B:H5O301 2.3 24.9 1.0 C10 B:H5O301 2.4 16.5 1.0 F1 B:H5O301 2.6 44.2 1.0 H16 B:H5O301 2.6 16.6 1.0 HG B:SER251 2.8 11.8 0.0 HB2 B:SER251 3.3 15.0 1.0 O B:HOH405 3.4 22.4 1.0 HB3 B:SER251 3.4 15.1 1.0 N1 A:H5O301 3.5 19.7 1.0 O A:HOH450 3.5 51.0 1.0 C13 B:H5O301 3.5 22.7 1.0 C9 B:H5O301 3.6 13.0 1.0 OG B:SER251 3.6 20.1 1.0 CB B:SER251 3.6 14.9 1.0 N2 A:H5O301 4.0 19.1 1.0 HG22 B:VAL160 4.0 11.9 1.0 C14 B:H5O301 4.1 18.4 1.0 HB B:VAL160 4.2 11.4 1.0 HG12 B:VAL160 4.3 12.9 1.0 C8 A:H5O301 4.3 15.6 1.0 O A:HOH443 4.3 16.4 1.0 H16 A:H5O301 4.3 14.9 1.0 F2 B:H5O301 4.5 25.8 1.0 O B:HOH419 4.6 24.7 1.0 C10 A:H5O301 4.6 15.0 1.0 C9 A:H5O301 4.6 11.6 1.0 CG2 B:VAL160 4.7 12.5 1.0 CB B:VAL160 4.8 11.4 1.0 HG23 B:VAL160 4.8 12.4 1.0 C8 B:H5O301 4.8 13.2 1.0 CG1 B:VAL160 4.9 12.8 1.0 OD2 B:ASP162 4.9 30.6 1.0 N A:H5O301 4.9 13.3 1.0 HG11 B:VAL160 5.0 12.5 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