Bromine in PDB 8r41: Structure of CHI3L1 in Complex with Inhibitor 1

The structure of Structure of CHI3L1 in Complex with Inhibitor 1, PDB code: 8r41 was solved by E.Nowak, A.Napiorkowska-Gromadzka, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.57 / 2.25
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.36, 122.25, 136.73, 90, 90, 90
R / Rfree (%)	20.5 / 23.4

The binding sites of Bromine atom in the Structure of CHI3L1 in Complex with Inhibitor 1 (pdb code 8r41). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Structure of CHI3L1 in Complex with Inhibitor 1, PDB code: 8r41:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Structure of CHI3L1 in Complex with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of CHI3L1 in Complex with Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br401 b:50.1 occ:0.50 BR25 A:XUF401 0.0 50.1 0.5 C22 A:XUF401 1.9 53.5 1.0 C21 A:XUF401 2.8 53.5 1.0 C23 A:XUF401 2.9 56.3 1.0 OG1 A:THR293 3.1 60.2 1.0 OG1 A:THR288 3.4 52.9 1.0 CB A:THR288 3.4 56.7 1.0 CG2 A:THR288 3.6 48.4 1.0 CB A:THR293 3.6 54.6 1.0 C A:THR293 3.9 48.5 1.0 N A:ALA295 4.0 49.4 1.0 C A:LEU294 4.0 51.8 1.0 N A:LEU294 4.0 48.2 1.0 O A:THR293 4.0 52.2 1.0 C20 A:XUF401 4.1 51.3 1.0 C24 A:XUF401 4.2 60.0 1.0 CA A:LEU294 4.2 46.2 1.0 CD2 A:LEU356 4.4 43.6 1.0 O A:HOH508 4.4 48.3 1.0 CA A:THR293 4.4 50.0 1.0 O A:LEU294 4.5 49.5 1.0 C2 A:EDO402 4.5 65.2 1.0 OE1 A:GLU298 4.7 51.2 1.0 C19 A:XUF401 4.7 54.7 1.0 CA A:ALA295 4.7 45.0 1.0 CG2 A:THR293 4.8 46.6 1.0 CA A:THR288 4.9 53.7 1.0 CB A:ALA295 5.0 44.1 1.0

Bromine binding site 2 out of 4 in the Structure of CHI3L1 in Complex with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of CHI3L1 in Complex with Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br406 b:81.4 occ:0.50 OH A:TYR239 3.5 46.5 1.0 NH2 A:ARG233 3.7 50.6 1.0 NH2 A:ARG246 3.8 52.1 1.0 NE A:ARG233 4.1 55.2 1.0 CE A:LYS182 4.2 43.7 1.0 CZ A:ARG233 4.4 63.9 1.0 CZ A:TYR239 4.6 43.5 1.0 CE2 A:TYR239 4.8 36.8 1.0

Bromine binding site 3 out of 4 in the Structure of CHI3L1 in Complex with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of CHI3L1 in Complex with Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br407 b:93.8 occ:1.00 O A:HOH591 3.9 67.0 1.0 NH2 A:ARG233 3.9 50.6 1.0 NH1 A:ARG233 3.9 60.5 1.0 CZ A:ARG233 4.4 63.9 1.0

Bromine binding site 4 out of 4 in the Structure of CHI3L1 in Complex with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of CHI3L1 in Complex with Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br401 b:51.6 occ:0.50 BR25 B:XUF401 0.0 51.6 0.5 C22 B:XUF401 1.9 62.7 1.0 C23 B:XUF401 2.8 64.9 1.0 C21 B:XUF401 2.9 59.4 1.0 OG1 B:THR293 3.3 66.3 1.0 CG2 B:THR293 3.4 62.9 1.0 CB B:THR288 3.5 61.2 1.0 CG2 B:THR288 3.6 62.9 1.0 OG1 B:THR288 3.7 58.5 1.0 CB B:THR293 3.9 59.6 1.0 N B:LEU294 4.0 51.3 1.0 C B:LEU294 4.0 56.8 1.0 C B:THR293 4.1 54.1 1.0 N B:ALA295 4.1 56.3 1.0 C24 B:XUF401 4.2 65.0 1.0 C20 B:XUF401 4.2 61.5 1.0 CA B:LEU294 4.2 55.9 1.0 O B:THR293 4.3 56.5 1.0 CD2 B:LEU356 4.3 52.0 1.0 O B:LEU294 4.4 58.0 1.0 O B:HOH508 4.5 59.7 1.0 CA B:THR293 4.6 55.4 1.0 C19 B:XUF401 4.7 64.2 1.0 C2 B:EDO403 4.8 68.8 1.0 CA B:ALA295 4.8 55.8 1.0 OE1 B:GLU298 4.8 58.9 1.0 O1 B:EDO403 4.8 69.0 1.0 CB B:PHE261 4.9 51.1 1.0 CA B:THR288 4.9 62.2 1.0

W.Czestkowski, L.Krzeminski, M.C.Piotrowicz, M.Mazur, E.Pluta, G.Andryianau, R.Koralewski, K.Matyszewski, S.Olejniczak, M.Kowalski, K.Lisiecka, R.Koziel, K.Piwowar, D.Papiernik, M.Nowotny, A.Napiorkowska-Gromadzka, E.Nowak, D.Niedzialek, G.Wieczorek, A.Siwinska, T.Rejczak, K.Jedrzejczak, K.Mulewski, J.Olczak, Z.Zaslona, A.Golebiowski, K.Drzewicka, A.Bartoszewicz. Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38427954
DOI: 10.1021/ACS.JMEDCHEM.3C02255