Chlorine 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
Fluorine	(F)	3 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human Galectin-3 Crd in Complex with Novel Tetrahydropyran-Based Thiodisaccharide Mimic Inhibitor, PDB code: 7df5:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl302 b:18.3 occ:1.00 O A:HOH541 2.2 39.3 1.0 H15 A:H5O306 2.8 13.6 1.0 HD21 A:ASN160 2.9 11.9 0.0 HE A:ARG162 3.2 12.4 1.0 H17 A:H5O306 3.2 13.7 1.0 H10 A:H5O306 3.2 19.6 1.0 HG2 A:ARG162 3.3 12.8 1.0 OD1 A:ASN160 3.4 12.2 1.0 H14 A:H5O306 3.5 10.8 0.0 NE A:ARG162 3.5 12.7 1.0 H A:H5O306 3.6 14.6 1.0 HD2 A:ARG144 3.6 16.8 1.0 C7 A:H5O306 3.7 13.1 1.0 ND2 A:ASN160 3.7 12.0 1.0 HB2 A:ARG144 3.8 14.2 1.0 HH21 A:ARG162 3.9 12.6 1.0 C14 A:H5O306 4.0 13.2 1.0 CG A:ASN160 4.0 11.0 1.0 CZ A:ARG162 4.0 12.4 1.0 HD3 A:ARG162 4.0 12.9 1.0 HB3 A:ARG144 4.1 13.9 1.0 HH21 A:ARG144 4.1 27.7 1.0 CG A:ARG162 4.1 12.7 1.0 NH2 A:ARG162 4.1 12.7 1.0 CD A:ARG162 4.1 12.9 1.0 C A:H5O306 4.3 20.1 1.0 CB A:ARG144 4.4 14.5 1.0 HD22 A:ASN160 4.4 11.9 0.0 C8 A:H5O306 4.4 14.7 1.0 O3 A:H5O306 4.4 11.2 1.0 HD3 A:ARG144 4.5 16.5 1.0 CD A:ARG144 4.5 15.9 1.0 H8 A:H5O306 4.5 19.7 1.0 HG3 A:ARG162 4.5 12.8 1.0 C9 A:H5O306 4.5 14.7 1.0 C1 A:H5O306 4.6 14.4 1.0 N A:H5O306 4.7 13.3 1.0 HH22 A:ARG162 4.7 12.6 1.0 C13 A:H5O306 4.8 13.6 1.0 F2 A:H5O306 4.9 14.6 1.0 O A:HOH447 4.9 33.4 1.0 NH1 A:ARG162 4.9 13.6 1.0 H9 A:H5O306 4.9 19.7 1.0 O A:H5O306 5.0 17.6 1.0 NH2 A:ARG144 5.0 28.9 1.0

Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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:Cl303 b:54.7 occ:1.00 O A:HOH412 2.2 21.7 1.0 HH11 A:ARG169 2.6 17.1 1.0 H A:SER194 2.7 12.1 1.0 HD2 A:PHE163 2.8 16.0 1.0 OG A:SER194 3.2 20.1 1.0 O A:HOH411 3.2 49.2 1.0 HG A:SER194 3.2 20.6 0.0 NH1 A:ARG169 3.3 20.2 1.0 HB2 A:SER194 3.3 15.8 1.0 HH12 A:ARG169 3.4 16.9 1.0 N A:SER194 3.6 12.2 1.0 HD3 A:ARG169 3.6 14.0 1.0 CD2 A:PHE163 3.7 14.7 1.0 CB A:SER194 3.7 16.0 1.0 HE2 A:PHE163 3.8 14.6 1.0 HA A:GLU193 3.8 11.7 1.0 HD2 A:ARG169 4.0 14.8 1.0 CE2 A:PHE163 4.2 15.0 1.0 CD A:ARG169 4.2 14.2 1.0 HB3 A:PHE163 4.3 13.1 1.0 CA A:SER194 4.3 12.1 1.0 CZ A:ARG169 4.4 14.2 1.0 OE1 A:GLU193 4.5 17.7 1.0 HB3 A:SER194 4.6 15.7 1.0 C A:GLU193 4.6 11.5 1.0 CA A:GLU193 4.7 11.6 1.0 NE A:ARG169 4.8 15.4 1.0 HA A:SER194 4.8 12.4 1.0 CG A:PHE163 4.8 13.2 1.0 HE1 A:PHE190 5.0 11.8 1.0

Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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:Cl304 b:23.4 occ:1.00 H A:LYS226 2.4 10.1 1.0 H A:LYS227 2.6 9.5 1.0 HG13 A:VAL225 2.9 11.2 1.0 HG3 A:LYS227 3.0 13.3 1.0 O A:HOH567 3.1 14.8 1.0 N A:LYS226 3.3 9.8 1.0 HB2 A:LYS227 3.3 11.4 1.0 O A:HOH543 3.3 34.1 1.0 HD2 A:LYS227 3.4 18.3 1.0 HA A:VAL225 3.4 9.9 1.0 N A:LYS227 3.4 9.3 1.0 HB2 A:LYS226 3.7 15.6 1.0 CG A:LYS227 3.7 13.2 1.0 CG1 A:VAL225 3.8 11.2 1.0 CB A:LYS227 3.9 11.5 1.0 CD A:LYS227 4.0 18.1 1.0 HG11 A:VAL225 4.0 11.2 1.0 HH11 A:ARG151 4.0 10.3 1.0 HG2 A:LYS226 4.0 18.1 1.0 NH1 A:ARG151 4.1 10.5 1.0 CA A:LYS226 4.1 10.5 1.0 C A:VAL225 4.1 10.5 1.0 CA A:VAL225 4.1 9.6 1.0 C A:LYS226 4.2 9.5 1.0 CB A:LYS226 4.2 15.2 1.0 HE3 A:LYS227 4.2 26.3 1.0 HD3 A:ARG151 4.3 9.6 1.0 CZ A:ARG151 4.3 9.9 1.0 HH12 A:ARG151 4.3 10.2 1.0 CA A:LYS227 4.3 9.8 1.0 HG12 A:VAL225 4.4 10.9 1.0 O A:HOH452 4.5 11.4 1.0 NE A:ARG151 4.5 9.9 1.0 CB A:VAL225 4.5 10.3 1.0 CG A:LYS226 4.5 18.6 1.0 HG2 A:LYS227 4.6 13.3 1.0 HG21 A:VAL225 4.6 10.5 1.0 O A:HOH468 4.6 15.8 1.0 CE A:LYS227 4.6 27.0 1.0 HD2 A:ARG151 4.7 9.6 1.0 HG3 A:LYS226 4.7 18.5 1.0 HZ1 A:LYS227 4.7 31.4 1.0 CD A:ARG151 4.7 9.5 1.0 HB3 A:LYS227 4.8 11.4 1.0 HD3 A:LYS227 4.8 18.1 1.0 NH2 A:ARG151 4.9 11.2 1.0 HA A:LYS227 4.9 9.8 1.0 HE A:ARG151 5.0 9.8 1.0 HA A:LYS226 5.0 10.4 1.0

Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl305 b:19.4 occ:1.00 H A:GLY152 2.3 9.6 1.0 H A:SER232 2.8 9.2 1.0 HB2 A:SER232 3.0 10.7 1.0 HG3 A:LYS233 3.0 16.8 1.0 O A:HOH584 3.0 16.4 1.0 N A:GLY152 3.1 9.8 1.0 O A:GLN150 3.3 9.9 1.0 HA A:ARG151 3.3 8.9 1.0 O A:HOH497 3.4 63.2 1.0 HA2 A:GLY152 3.6 10.0 1.0 H A:LYS233 3.6 9.6 1.0 N A:SER232 3.6 9.2 1.0 HB2 A:LYS233 3.7 13.2 1.0 HD2 A:LYS233 3.7 26.5 1.0 HB2 A:GLN150 3.7 13.9 1.0 N A:LYS233 3.8 9.3 1.0 CB A:SER232 3.8 10.3 1.0 CG A:LYS233 3.8 17.0 1.0 C A:SER232 3.8 10.0 1.0 C A:GLN150 3.8 8.3 1.0 CA A:SER232 3.9 10.1 1.0 CA A:GLY152 3.9 10.0 1.0 CA A:ARG151 4.0 8.9 1.0 O A:GLU230 4.0 9.4 1.0 C A:ARG151 4.0 8.5 1.0 HB3 A:GLN150 4.1 20.9 1.0 CB A:LYS233 4.2 13.2 1.0 CD A:LYS233 4.2 23.0 1.0 N A:ARG151 4.2 8.8 1.0 CB A:GLN150 4.3 13.1 1.0 HB3 A:SER232 4.4 10.2 1.0 O A:GLY152 4.5 11.5 1.0 O A:SER232 4.5 10.8 1.0 HA A:ILE231 4.5 9.4 1.0 HG2 A:LYS233 4.6 16.9 1.0 CA A:LYS233 4.6 10.2 1.0 OG A:SER232 4.6 11.1 1.0 HA3 A:GLY152 4.7 10.0 1.0 C A:GLY152 4.7 9.9 1.0 C A:ILE231 4.8 9.0 1.0 CA A:GLN150 4.8 9.8 1.0 HG A:SER232 4.8 11.4 0.0 HA A:SER232 4.9 10.0 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