Fluorine in PDB 6qlp: Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 3

The structure of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 3, PDB code: 6qlp 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)	42.26 / 1.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.782, 57.276, 62.610, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.1

The structure of Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 3 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

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

Fluorine binding site 1 out of 3 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 3


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 Substituted Polyfluoroaryl Monothiogalactoside Derivative 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:24.2 occ:1.00 F21 A:J3Q302 0.0 24.2 1.0 C20 A:J3Q302 1.3 20.8 1.0 C22 A:J3Q302 2.3 21.0 1.0 C19 A:J3Q302 2.4 19.8 1.0 H191 A:J3Q302 2.6 23.8 1.0 F23 A:J3Q302 2.7 24.4 1.0 HB3 A:SER237 2.9 17.4 0.6 HB2 A:SER237 3.1 20.2 0.4 O A:HOH532 3.2 40.0 1.0 OG A:SER237 3.4 16.3 0.4 O A:HOH424 3.4 31.7 1.0 NH2 A:ARG144 3.5 34.2 1.0 HH22 A:ARG144 3.5 41.1 1.0 HH21 A:ARG144 3.5 41.1 1.0 C24 A:J3Q302 3.6 18.9 1.0 HB2 A:SER237 3.6 17.4 0.6 C18 A:J3Q302 3.6 17.8 1.0 CB A:SER237 3.6 14.5 0.6 CB A:SER237 3.7 16.8 0.4 O A:HOH522 3.8 32.7 1.0 HG A:SER237 3.8 18.6 0.6 CZ A:ARG144 3.9 33.1 1.0 C26 A:J3Q302 4.1 17.2 1.0 HG A:SER237 4.2 19.5 0.4 OG A:SER237 4.2 15.5 0.6 HB3 A:SER237 4.2 20.2 0.4 NH1 A:ARG144 4.3 34.7 1.0 HH12 A:ARG144 4.3 41.7 1.0 NE A:ARG144 4.4 28.9 1.0 O A:HOH489 4.5 28.4 1.0 HE A:ARG144 4.5 34.7 1.0 F25 A:J3Q302 4.6 19.7 1.0 H A:GLY238 4.6 18.8 1.0 O A:HOH431 4.7 26.0 1.0 HA2 A:GLY238 4.7 19.1 1.0 HB3 A:ALA146 4.7 16.5 1.0 N A:GLY238 4.8 15.6 1.0 C17 A:J3Q302 4.8 19.0 1.0 HH11 A:ARG144 4.9 41.7 1.0 HG3 A:PRO117 4.9 31.8 1.0 CA A:SER237 4.9 14.3 0.6 CA A:SER237 5.0 15.4 0.4

Fluorine binding site 2 out of 3 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 3


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 Substituted Polyfluoroaryl Monothiogalactoside Derivative 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:24.4 occ:1.00 F23 A:J3Q302 0.0 24.4 1.0 C22 A:J3Q302 1.3 21.0 1.0 C20 A:J3Q302 2.4 20.8 1.0 C24 A:J3Q302 2.4 18.9 1.0 HA2 A:GLY238 2.5 19.1 1.0 F25 A:J3Q302 2.7 19.7 1.0 F21 A:J3Q302 2.7 24.2 1.0 HB3 A:SER237 2.9 17.4 0.6 HA3 A:GLY238 2.9 19.1 1.0 CA A:GLY238 2.9 16.0 1.0 N A:GLY238 3.0 15.6 1.0 HB2 A:SER237 3.1 17.4 0.6 HG3 A:ARG144 3.1 24.6 1.0 HB2 A:SER237 3.2 20.2 0.4 OG A:SER237 3.3 16.3 0.4 H A:GLY238 3.3 18.8 1.0 C A:SER237 3.4 14.6 1.0 CB A:SER237 3.4 14.5 0.6 HE A:ARG144 3.4 34.7 1.0 NE A:ARG144 3.6 28.9 1.0 C26 A:J3Q302 3.6 17.2 1.0 C19 A:J3Q302 3.6 19.8 1.0 CB A:SER237 3.6 16.8 0.4 O A:SER237 3.7 14.5 1.0 HB3 A:ALA146 3.9 16.5 1.0 CZ A:ARG144 3.9 33.1 1.0 HH21 A:ARG144 3.9 41.1 1.0 O A:HOH433 3.9 34.6 1.0 HG A:SER237 4.0 19.5 0.4 CG A:ARG144 4.0 20.5 1.0 CA A:SER237 4.0 14.3 0.6 HD2 A:ARG144 4.1 29.6 1.0 NH2 A:ARG144 4.1 34.2 1.0 H A:ALA146 4.1 14.3 1.0 CA A:SER237 4.1 15.4 0.4 CD A:ARG144 4.1 24.7 1.0 C18 A:J3Q302 4.1 17.8 1.0 HA A:ILE145 4.1 16.2 1.0 O A:HOH489 4.3 28.4 1.0 HB2 A:ALA146 4.3 16.5 1.0 N A:ALA146 4.4 12.0 1.0 C A:GLY238 4.4 14.7 1.0 H261 A:J3Q302 4.4 20.6 1.0 H191 A:J3Q302 4.5 23.8 1.0 HB3 A:SER237 4.5 20.2 0.4 HG2 A:ARG144 4.5 24.6 1.0 CB A:ALA146 4.5 13.7 1.0 HA A:SER237 4.6 17.2 0.6 O A:ARG144 4.6 15.3 1.0 OG A:SER237 4.6 15.5 0.6 HH22 A:ARG144 4.6 41.1 1.0 HB2 A:ARG144 4.6 20.4 1.0 O A:HOH532 4.7 40.0 1.0 HG A:SER237 4.7 18.6 0.6 C A:ILE145 4.7 12.5 1.0 HA A:SER237 4.7 18.5 0.4 NH1 A:ARG144 4.7 34.7 1.0 CA A:ILE145 4.8 13.5 1.0 H A:ASP239 4.9 16.7 1.0 C A:ARG144 4.9 14.7 1.0 HH11 A:ARG144 4.9 41.7 1.0 CB A:ARG144 4.9 17.0 1.0

Fluorine binding site 3 out of 3 in the Galectin-3C in Complex with Substituted Polyfluoroaryl Monothiogalactoside Derivative 3


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 Substituted Polyfluoroaryl Monothiogalactoside Derivative 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F302 b:19.7 occ:1.00 F25 A:J3Q302 0.0 19.7 1.0 C24 A:J3Q302 1.3 18.9 1.0 C22 A:J3Q302 2.3 21.0 1.0 C26 A:J3Q302 2.3 17.2 1.0 H261 A:J3Q302 2.5 20.6 1.0 HG3 A:ARG144 2.6 24.6 1.0 HB2 A:ARG144 2.6 20.4 1.0 F23 A:J3Q302 2.7 24.4 1.0 HB2 A:ALA146 2.8 16.5 1.0 C A:ILE145 3.0 12.5 1.0 HD2 A:ARG144 3.2 29.6 1.0 CG A:ARG144 3.2 20.5 1.0 O A:ILE145 3.2 12.6 1.0 CB A:ARG144 3.3 17.0 1.0 HD22 A:ASN160 3.3 15.8 1.0 HD21 A:ASN160 3.3 15.8 1.0 N A:ALA146 3.3 12.0 1.0 N A:ILE145 3.3 13.4 1.0 HA A:ILE145 3.4 16.2 1.0 CA A:ILE145 3.5 13.5 1.0 HB3 A:ALA146 3.5 16.5 1.0 CB A:ALA146 3.5 13.7 1.0 C20 A:J3Q302 3.6 20.8 1.0 ND2 A:ASN160 3.6 13.2 1.0 H A:ILE145 3.6 16.1 1.0 C A:ARG144 3.6 14.7 1.0 CD A:ARG144 3.6 24.7 1.0 C18 A:J3Q302 3.6 17.8 1.0 H A:ALA146 3.6 14.3 1.0 HA3 A:GLY238 3.8 19.1 1.0 CA A:ALA146 4.0 12.4 1.0 CA A:ARG144 4.0 15.5 1.0 O A:ARG144 4.0 15.3 1.0 C19 A:J3Q302 4.0 19.8 1.0 HB3 A:ARG144 4.1 20.4 1.0 NE A:ARG144 4.1 28.9 1.0 HG2 A:ARG144 4.1 24.6 1.0 HA2 A:GLY238 4.3 19.1 1.0 HE A:ARG144 4.3 34.7 1.0 HA A:ALA146 4.3 14.9 1.0 HB1 A:ALA146 4.4 16.5 1.0 HA A:ARG144 4.4 18.6 1.0 CA A:GLY238 4.5 16.0 1.0 HB2 A:SER237 4.5 17.4 0.6 HD3 A:ARG144 4.5 29.6 1.0 O A:SER237 4.5 14.5 1.0 CL A:CL303 4.6 29.9 1.0 F21 A:J3Q302 4.6 24.2 1.0 OG A:SER237 4.6 16.3 0.4 HH11 A:ARG144 4.7 41.7 1.0 CZ A:ARG144 4.7 33.1 1.0 CG A:ASN160 4.7 13.3 1.0 C17 A:J3Q302 4.8 19.0 1.0 C A:SER237 4.8 14.6 1.0 NH1 A:ARG144 4.9 34.7 1.0 N A:GLY238 4.9 15.6 1.0 O A:HOH473 4.9 38.9 1.0 CB A:ILE145 5.0 13.9 1.0 H161 A:J3Q302 5.0 21.8 1.0

R.Kumar, M.M.Ignjatovic, K.Peterson, M.Olsson, H.Leffler, U.Ryde, U.J.Nilsson, D.T.Logan. Structure and Energetics of Ligand-Fluorine Interactions with Galectin-3 Backbone and Side-Chain Amides: Insight Into Solvation Effects and Multipolar Interactions. Chemmedchem V. 14 1528 2019.
ISSN: ESSN 1860-7187
PubMed: 31246331
DOI: 10.1002/CMDC.201900293