Chlorine in PDB 8r4x: Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30

The structure of Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30, PDB code: 8r4x 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)	36.03 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.18, 121.39, 134.3, 90, 90, 90
R / Rfree (%)	17 / 19

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Chlorine atom in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30 (pdb code 8r4x). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30, PDB code: 8r4x:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:23.8 occ:1.00 CL20 A:XZ0408 0.0 23.8 1.0 C18 A:XZ0408 1.7 20.0 1.0 C17 A:XZ0408 2.7 19.2 1.0 C19 A:XZ0408 2.7 20.6 1.0 CB A:ALA138 3.3 21.9 1.0 CB A:ALA177 3.6 20.1 1.0 CE1 A:PHE58 3.6 19.7 1.0 CZ A:PHE58 3.7 21.2 1.0 C16 A:XZ0408 4.0 18.3 1.0 C14 A:XZ0408 4.0 18.4 1.0 OG A:SER95 4.1 19.6 1.0 CD1 A:LEU140 4.2 35.7 1.0 CA A:ALA138 4.3 20.9 1.0 OH A:TYR27 4.3 20.8 1.0 CD2 A:LEU140 4.4 29.3 1.0 N15 A:XZ0408 4.4 20.0 1.0 CE2 A:TYR27 4.5 18.4 1.0 OD2 A:ASP136 4.5 21.8 1.0 CZ3 A:TRP352 4.6 21.0 1.0 CZ A:TYR27 4.6 20.0 1.0 CG A:LEU140 4.7 31.3 1.0 SD A:MET204 4.7 25.9 1.0 CD1 A:PHE58 5.0 19.3 1.0

Chlorine binding site 2 out of 11 in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:27.1 occ:1.00 CL28 A:XZ0408 0.0 27.1 1.0 C25 A:XZ0408 1.8 22.4 1.0 C24 A:XZ0408 2.7 22.6 1.0 C26 A:XZ0408 2.7 25.7 1.0 OG1 A:THR293 3.3 27.8 1.0 CB A:THR288 3.5 26.1 1.0 OG1 A:THR288 3.6 22.2 1.0 N A:ALA295 3.6 19.8 1.0 CG2 A:THR288 3.7 24.8 1.0 C A:LEU294 3.7 21.4 1.0 CB A:THR293 3.8 22.8 1.0 CD2 A:LEU356 4.0 20.3 1.0 N A:LEU294 4.0 22.0 1.0 C23 A:XZ0408 4.0 20.5 1.0 C27 A:XZ0408 4.1 24.5 1.0 CA A:LEU294 4.1 22.4 1.0 O A:LEU294 4.2 21.5 1.0 C A:THR293 4.2 19.0 1.0 CA A:ALA295 4.3 20.3 1.0 C22 A:XZ0408 4.5 19.9 1.0 O A:HOH632 4.5 34.7 1.0 O A:THR293 4.6 23.0 1.0 CB A:ALA295 4.6 22.0 1.0 CB A:PHE261 4.6 19.9 1.0 CA A:THR293 4.7 20.1 1.0 OE1 A:GLU298 4.7 23.1 1.0 O A:HOH551 4.7 23.8 1.0 CD1 A:LEU356 4.9 20.3 1.0 CG2 A:THR293 5.0 28.4 1.0

Chlorine binding site 3 out of 11 in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl405 b:23.1 occ:1.00 CL20 B:XZ0405 0.0 23.1 1.0 C18 B:XZ0405 1.8 18.6 1.0 C17 B:XZ0405 2.7 20.0 1.0 C19 B:XZ0405 2.7 20.8 1.0 CB B:ALA138 3.3 23.0 1.0 CB B:ALA177 3.5 22.4 1.0 CE1 B:PHE58 3.6 22.4 1.0 CZ B:PHE58 3.7 20.6 1.0 C14 B:XZ0405 4.0 19.7 1.0 C16 B:XZ0405 4.0 19.5 1.0 CD1 B:LEU140 4.0 29.5 1.0 OG B:SER95 4.1 20.3 1.0 OH B:TYR27 4.2 20.4 1.0 CE2 B:TYR27 4.3 18.9 1.0 CA B:ALA138 4.3 21.8 1.0 CZ3 B:TRP352 4.4 19.7 1.0 CD2 B:LEU140 4.4 25.9 1.0 OD2 B:ASP136 4.4 22.8 1.0 CZ B:TYR27 4.5 20.6 1.0 N15 B:XZ0405 4.5 19.6 1.0 CG B:LEU140 4.7 30.1 1.0 SD B:MET204 4.9 33.0 1.0 CD1 B:PHE58 5.0 20.5 1.0

Chlorine binding site 4 out of 11 in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl405 b:26.4 occ:1.00 CL28 B:XZ0405 0.0 26.4 1.0 C25 B:XZ0405 1.8 20.9 1.0 C26 B:XZ0405 2.7 24.1 1.0 C24 B:XZ0405 2.7 21.2 1.0 OG1 B:THR293 3.3 25.9 1.0 CB B:THR288 3.6 22.2 1.0 OG1 B:THR288 3.6 22.3 1.0 CB B:THR293 3.7 21.9 1.0 CG2 B:THR288 3.7 24.6 1.0 N B:ALA295 3.7 21.4 1.0 C B:LEU294 3.9 19.2 1.0 CD2 B:LEU356 3.9 21.7 1.0 C27 B:XZ0405 4.0 22.4 1.0 C23 B:XZ0405 4.0 20.5 1.0 N B:LEU294 4.1 21.0 1.0 CA B:LEU294 4.2 20.1 1.0 C B:THR293 4.3 18.8 1.0 O B:LEU294 4.3 20.9 1.0 CA B:ALA295 4.4 20.6 1.0 O B:HOH656 4.4 36.0 1.0 C22 B:XZ0405 4.5 19.4 1.0 CA B:THR293 4.6 22.9 1.0 CB B:PHE261 4.7 20.2 1.0 O B:THR293 4.7 21.9 1.0 OE1 B:GLU298 4.7 23.4 1.0 CB B:ALA295 4.7 23.7 1.0 CD1 B:LEU356 4.7 19.9 1.0 O B:HOH533 4.8 23.4 1.0 CG2 B:THR293 4.8 24.2 1.0 CG B:LEU356 4.9 22.7 1.0

Chlorine binding site 5 out of 11 in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl406 b:56.9 occ:1.00 O C:HOH551 2.2 59.6 1.0 OE2 B:GLU227 3.3 42.3 1.0 O2 C:EDO401 3.6 48.9 1.0 NH2 C:ARG233 3.6 52.8 1.0 NE C:ARG233 4.0 36.0 1.0 O1 C:EDO401 4.0 68.7 1.0 NH2 D:ARG246 4.1 43.6 1.0 C2 C:EDO401 4.2 50.8 1.0 OH C:TYR239 4.2 34.8 1.0 CE1 C:TYR239 4.2 26.9 1.0 CZ C:ARG233 4.3 48.1 1.0 NH1 D:ARG246 4.3 44.9 1.0 CD B:GLU227 4.3 45.6 1.0 OE1 B:GLU227 4.5 41.8 1.0 CZ D:ARG246 4.7 45.9 1.0 O C:HOH764 4.7 51.8 1.0 CZ C:TYR239 4.7 26.8 1.0 C1 C:EDO401 4.8 52.7 1.0 NH2 C:ARG246 4.9 43.7 1.0

Chlorine binding site 6 out of 11 in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl407 b:53.3 occ:1.00 NH1 A:ARG233 2.7 61.6 1.0 NH2 B:ARG246 3.5 35.9 0.5 OH B:TYR239 3.5 28.6 1.0 CZ A:ARG233 3.5 62.9 1.0 NH1 B:ARG233 3.5 62.4 1.0 NH2 A:ARG233 3.6 58.9 1.0 CE1 A:PHE234 3.7 20.6 0.5 CZ A:PHE234 3.9 19.5 0.5 NH1 B:ARG246 4.0 18.0 0.5 CE A:LYS182 4.1 32.1 1.0 OH A:TYR239 4.1 32.5 1.0 CZ B:ARG246 4.2 27.2 0.5 CZ B:ARG233 4.2 73.5 1.0 CE B:LYS182 4.2 34.5 1.0 CZ B:TYR239 4.5 29.3 1.0 NH2 B:ARG233 4.5 68.1 1.0 CE1 B:TYR239 4.6 29.8 1.0 CE1 B:TYR243 4.6 26.4 1.0 O B:HOH593 4.6 40.0 1.0 NE A:ARG233 4.7 54.1 1.0 NH2 B:ARG246 4.7 22.4 0.5 CE2 A:TYR239 4.9 30.7 1.0 CD1 B:TYR243 4.9 28.1 1.0 NZ A:LYS182 4.9 33.4 1.0 CE1 B:PHE234 4.9 44.1 1.0 CD1 A:PHE234 4.9 22.9 0.5 NE B:ARG233 4.9 68.7 1.0 CZ A:TYR239 4.9 28.9 1.0 NZ B:LYS182 5.0 32.7 1.0

Chlorine binding site 7 out of 11 in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl402 b:28.9 occ:1.00 CL20 C:XZ0402 0.0 28.9 1.0 C18 C:XZ0402 1.8 24.4 1.0 C19 C:XZ0402 2.7 26.1 1.0 C17 C:XZ0402 2.7 23.2 1.0 CB C:ALA138 3.3 26.5 1.0 CE1 C:PHE58 3.6 25.7 1.0 CZ C:PHE58 3.7 25.2 1.0 CB C:ALA177 3.7 24.5 1.0 C14 C:XZ0402 3.9 23.5 1.0 C16 C:XZ0402 4.0 25.6 1.0 CD1 C:LEU140 4.2 39.9 1.0 CA C:ALA138 4.2 23.0 1.0 OG C:SER95 4.3 24.5 1.0 OH C:TYR27 4.4 25.2 1.0 N15 C:XZ0402 4.4 23.1 1.0 CD2 C:LEU140 4.4 34.8 1.0 CE2 C:TYR27 4.5 23.4 1.0 CZ3 C:TRP352 4.5 24.4 1.0 CZ C:TYR27 4.6 21.9 1.0 OD2 C:ASP136 4.7 27.2 1.0 CG C:LEU140 4.8 37.6 1.0 SD C:MET204 4.8 27.0 1.0 CD1 C:PHE58 4.9 26.0 1.0

Chlorine binding site 8 out of 11 in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl402 b:31.7 occ:1.00 CL28 C:XZ0402 0.0 31.7 1.0 C25 C:XZ0402 1.8 29.4 1.0 C24 C:XZ0402 2.7 28.7 1.0 C26 C:XZ0402 2.8 28.4 1.0 OG1 C:THR293 3.3 32.5 1.0 OG1 C:THR288 3.5 26.1 1.0 CB C:THR288 3.6 26.0 1.0 CG2 C:THR288 3.6 29.3 1.0 N C:ALA295 3.7 26.3 1.0 C C:LEU294 3.7 22.3 1.0 CB C:THR293 3.8 28.1 1.0 C23 C:XZ0402 4.0 26.0 1.0 N C:LEU294 4.0 22.8 1.0 CD2 C:LEU356 4.0 25.6 1.0 C27 C:XZ0402 4.1 30.8 1.0 CA C:LEU294 4.1 21.3 1.0 O C:LEU294 4.2 24.2 1.0 CA C:ALA295 4.3 23.4 1.0 C C:THR293 4.3 22.4 1.0 C22 C:XZ0402 4.5 24.4 1.0 O C:HOH576 4.5 40.3 1.0 OE1 C:GLU298 4.6 24.5 1.0 CB C:ALA295 4.6 25.9 1.0 O C:THR293 4.6 27.4 1.0 CB C:PHE261 4.6 23.3 1.0 O C:HOH530 4.7 27.9 1.0 CA C:THR293 4.7 20.7 1.0 CD1 C:LEU356 4.8 24.8 1.0 CG2 C:THR293 5.0 28.9 1.0

Chlorine binding site 9 out of 11 in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl403 b:66.2 occ:1.00 O C:HOH667 3.3 27.6 1.0 NH1 C:ARG224 3.7 25.1 1.0 OE2 C:GLU227 3.7 32.2 0.5 CZ B:ARG233 3.7 73.5 1.0 NH2 B:ARG233 3.7 68.1 1.0 CD B:ARG233 3.7 64.4 1.0 NH1 B:ARG233 4.0 62.4 1.0 O B:HOH799 4.1 58.6 1.0 NE B:ARG233 4.2 68.7 1.0 NH2 C:ARG224 4.3 23.6 1.0 CD C:GLU227 4.4 40.8 0.5 CZ C:ARG224 4.5 22.6 1.0 CB C:ARG233 4.5 23.8 1.0 CD C:ARG233 4.5 37.5 1.0 OE1 C:GLU227 4.6 45.1 0.5 NH1 C:ARG233 4.7 44.6 1.0 CG C:ARG233 4.8 27.2 1.0 N C:ARG233 4.9 21.1 1.0

Chlorine binding site 10 out of 11 in the Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of Chitinase-3-Like Protein 1 in Complex with Inhibitor 30 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl406 b:28.1 occ:1.00 CL20 D:XZ0406 0.0 28.1 1.0 C18 D:XZ0406 1.7 24.5 1.0 C19 D:XZ0406 2.6 26.4 1.0 C17 D:XZ0406 2.7 27.8 1.0 CB D:ALA138 3.3 29.0 1.0 CB D:ALA177 3.6 22.8 1.0 CE1 D:PHE58 3.6 25.8 1.0 CZ D:PHE58 3.7 25.4 1.0 C14 D:XZ0406 3.9 24.6 1.0 C16 D:XZ0406 4.0 26.2 1.0 CD1 D:LEU140 4.0 39.1 1.0 OG D:SER95 4.1 26.4 1.0 CA D:ALA138 4.2 26.2 1.0 OH D:TYR27 4.3 24.2 1.0 N15 D:XZ0406 4.4 25.7 1.0 CE2 D:TYR27 4.4 22.4 1.0 CD2 D:LEU140 4.5 36.7 1.0 OD2 D:ASP136 4.5 27.9 1.0 CZ3 D:TRP352 4.5 22.8 1.0 CZ D:TYR27 4.6 25.8 1.0 CG D:LEU140 4.6 35.0 1.0 SD D:MET204 4.8 31.3 1.0 CD1 D:PHE58 4.9 24.7 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