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Chlorine in PDB 6ze8: Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01

Enzymatic activity of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01

All present enzymatic activity of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01:
3.2.1.14;

Protein crystallography data

The structure of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01, PDB code: 6ze8 was solved by M.Nowotny, A.Bartlomiejczak, A.Napiorkowska-Gromadzka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.34 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.325, 93.744, 281.642, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 16.8

Other elements in 6ze8:

The structure of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 (pdb code 6ze8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01, PDB code: 6ze8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6ze8

Go back to Chlorine Binding Sites List in 6ze8
Chlorine binding site 1 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:22.2
occ:1.00
CL1 A:QGB401 0.0 22.2 1.0
C24 A:QGB401 1.7 15.8 1.0
C23 A:QGB401 2.7 19.0 1.0
C25 A:QGB401 2.7 15.9 1.0
CB A:MET300 3.6 24.3 0.4
CG2 A:THR295 3.6 17.2 1.0
CB A:THR295 3.6 15.3 1.0
CB A:MET300 3.7 18.7 0.6
OG1 A:THR295 3.9 16.5 1.0
C26 A:QGB401 4.0 15.2 1.0
C22 A:QGB401 4.0 15.9 1.0
CD2 A:LEU362 4.1 14.1 1.0
N A:ALA302 4.2 13.1 1.0
C A:LEU301 4.3 15.8 1.0
O A:HOH642 4.3 19.7 1.0
N A:LEU301 4.3 15.6 1.0
CG A:MET300 4.3 30.6 0.4
C A:MET300 4.4 16.7 1.0
CG A:MET300 4.4 20.6 0.6
CA A:LEU301 4.5 13.4 1.0
C21 A:QGB401 4.6 15.6 1.0
CA A:MET300 4.7 18.1 0.4
O A:LEU301 4.7 16.9 1.0
CD1 A:LEU362 4.7 14.8 1.0
CA A:MET300 4.7 15.1 0.6
O A:MET300 4.7 16.5 1.0
CB A:TYR267 4.8 14.8 1.0
O A:HOH744 4.8 17.5 1.0
CA A:ALA302 4.8 14.2 1.0

Chlorine binding site 2 out of 6 in 6ze8

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Chlorine binding site 2 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:20.3
occ:1.00
CL1 B:QGB401 0.0 20.3 1.0
C24 B:QGB401 1.8 17.0 1.0
C23 B:QGB401 2.7 16.6 1.0
C25 B:QGB401 2.7 16.3 1.0
CB B:MET300 3.6 18.8 1.0
CB B:THR295 3.6 17.0 1.0
OG1 B:THR295 3.7 18.0 1.0
CG2 B:THR295 3.8 17.0 1.0
CD2 B:LEU362 4.0 15.7 1.0
C22 B:QGB401 4.0 16.1 1.0
C26 B:QGB401 4.0 16.2 1.0
N B:ALA302 4.1 14.9 1.0
C B:LEU301 4.2 16.1 1.0
N B:LEU301 4.2 14.9 1.0
C B:MET300 4.3 14.3 1.0
O B:HOH564 4.3 26.9 1.0
CA B:LEU301 4.4 15.8 1.0
CG B:MET300 4.4 25.1 1.0
C21 B:QGB401 4.6 14.5 1.0
O B:MET300 4.6 15.8 1.0
CA B:MET300 4.6 16.0 1.0
O B:LEU301 4.7 16.2 1.0
CA B:ALA302 4.8 14.3 1.0
CD1 B:LEU362 4.9 15.4 1.0
O B:HOH536 4.9 16.1 1.0
CB B:TYR267 4.9 13.3 1.0
OE1 B:GLU305 5.0 17.9 1.0

Chlorine binding site 3 out of 6 in 6ze8

Go back to Chlorine Binding Sites List in 6ze8
Chlorine binding site 3 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:21.6
occ:1.00
CL1 C:QGB401 0.0 21.6 1.0
C24 C:QGB401 1.8 15.2 1.0
C23 C:QGB401 2.7 13.1 1.0
C25 C:QGB401 2.8 15.6 1.0
CB C:MET300 3.6 21.3 0.4
CB C:THR295 3.6 16.0 1.0
CG2 C:THR295 3.7 15.9 1.0
CB C:MET300 3.7 18.6 0.6
OG1 C:THR295 3.9 16.4 1.0
C22 C:QGB401 4.0 13.0 1.0
CD2 C:LEU362 4.1 13.8 1.0
C26 C:QGB401 4.1 14.5 1.0
O C:HOH686 4.2 21.3 1.0
N C:ALA302 4.2 14.1 1.0
CG C:MET300 4.3 21.6 0.6
C C:LEU301 4.3 15.0 1.0
N C:LEU301 4.3 14.4 1.0
C C:MET300 4.4 14.0 0.6
CG C:MET300 4.4 25.2 0.4
C C:MET300 4.5 16.4 0.4
CA C:LEU301 4.5 13.5 1.0
C21 C:QGB401 4.6 13.1 1.0
CD1 C:LEU362 4.6 14.3 1.0
CA C:MET300 4.7 17.6 0.4
CB C:TYR267 4.7 13.2 1.0
O C:MET300 4.7 14.7 0.6
O C:LEU301 4.7 15.3 1.0
CA C:MET300 4.7 15.2 0.6
O C:HOH751 4.9 18.7 1.0
CA C:ALA302 4.9 14.1 1.0
O C:MET300 4.9 17.7 0.4
CG C:LEU362 5.0 13.1 1.0

Chlorine binding site 4 out of 6 in 6ze8

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Chlorine binding site 4 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:18.7
occ:1.00
CL1 D:QGB401 0.0 18.7 1.0
C24 D:QGB401 1.7 12.1 1.0
C25 D:QGB401 2.7 13.8 1.0
C23 D:QGB401 2.7 16.0 1.0
CB D:THR295 3.6 13.1 1.0
OG1 D:THR295 3.7 14.9 1.0
CB D:MET300 3.7 16.0 1.0
CG2 D:THR295 3.7 14.6 1.0
C26 D:QGB401 4.0 13.7 1.0
C22 D:QGB401 4.0 16.3 1.0
N D:ALA302 4.1 11.6 1.0
CD2 D:LEU362 4.1 13.8 1.0
C D:LEU301 4.2 12.4 1.0
N D:LEU301 4.2 13.1 1.0
C D:MET300 4.3 14.6 1.0
CA D:LEU301 4.4 11.9 1.0
O D:HOH567 4.4 26.5 1.0
CG D:MET300 4.5 22.9 1.0
O D:MET300 4.5 16.0 1.0
C21 D:QGB401 4.6 14.5 1.0
CA D:MET300 4.7 14.0 1.0
O D:LEU301 4.7 15.7 1.0
CA D:ALA302 4.8 13.0 1.0
O D:HOH556 4.8 15.1 1.0
CD1 D:LEU362 4.8 12.2 1.0
CB D:TYR267 4.9 12.2 1.0
OE1 D:GLU305 5.0 14.9 1.0

Chlorine binding site 5 out of 6 in 6ze8

Go back to Chlorine Binding Sites List in 6ze8
Chlorine binding site 5 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:18.8
occ:0.90
CL1 E:QGB401 0.0 18.8 0.9
C24 E:QGB401 1.7 16.3 1.0
C23 E:QGB401 2.7 15.6 1.0
C25 E:QGB401 2.7 16.8 1.0
CB E:MET300 3.6 20.8 0.5
CG2 E:THR295 3.6 16.0 1.0
CB E:THR295 3.7 14.1 1.0
CB E:MET300 3.7 20.2 0.6
OG1 E:THR295 3.9 14.5 1.0
C26 E:QGB401 4.0 15.2 1.0
C22 E:QGB401 4.0 15.4 1.0
CD2 E:LEU362 4.1 13.3 1.0
O E:HOH604 4.2 19.4 1.0
N E:ALA302 4.2 13.1 1.0
C E:LEU301 4.2 12.4 1.0
N E:LEU301 4.3 14.8 1.0
CG E:MET300 4.4 22.3 0.6
C E:MET300 4.4 13.6 0.6
C E:MET300 4.5 17.0 0.5
CG E:MET300 4.5 24.3 0.5
CA E:LEU301 4.5 13.6 1.0
C21 E:QGB401 4.6 15.3 1.0
CD1 E:LEU362 4.7 13.4 1.0
CA E:MET300 4.7 17.4 0.5
O E:LEU301 4.7 14.3 1.0
CB E:TYR267 4.7 13.6 1.0
O E:MET300 4.7 11.7 0.6
CA E:MET300 4.7 14.6 0.6
CA E:ALA302 4.9 13.6 1.0
O E:HOH769 4.9 16.9 1.0
O E:MET300 4.9 19.5 0.5
CG E:LEU362 5.0 11.5 1.0

Chlorine binding site 6 out of 6 in 6ze8

Go back to Chlorine Binding Sites List in 6ze8
Chlorine binding site 6 out of 6 in the Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human Chitotriosidase-1 (Hchit) Catalytic Domain in Complex with Compound Oatd-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl401

b:22.4
occ:1.00
CL1 F:QGB401 0.0 22.4 1.0
C24 F:QGB401 1.7 17.9 1.0
C23 F:QGB401 2.7 17.0 1.0
C25 F:QGB401 2.7 17.6 1.0
CG2 F:THR295 3.6 16.4 1.0
CB F:MET300 3.6 19.9 0.5
CB F:THR295 3.7 14.7 1.0
CB F:MET300 3.7 18.9 0.5
OG1 F:THR295 4.0 15.7 1.0
C26 F:QGB401 4.0 15.6 1.0
C22 F:QGB401 4.0 17.0 1.0
CD2 F:LEU362 4.1 14.8 1.0
O F:HOH657 4.2 20.2 1.0
N F:ALA302 4.3 14.8 1.0
C F:LEU301 4.4 15.0 1.0
CG F:MET300 4.4 19.7 0.5
C F:MET300 4.4 15.3 0.5
N F:LEU301 4.4 15.1 1.0
CG F:MET300 4.5 24.1 0.5
C F:MET300 4.5 14.6 0.5
C21 F:QGB401 4.5 15.8 1.0
CD1 F:LEU362 4.6 15.0 1.0
CA F:LEU301 4.7 14.4 1.0
CB F:TYR267 4.7 14.8 1.0
O F:MET300 4.7 18.1 0.5
O F:LEU301 4.7 15.4 1.0
CA F:MET300 4.7 15.7 0.5
CA F:MET300 4.8 14.7 0.5
O F:HOH741 4.8 19.0 1.0
CA F:ALA302 4.9 14.8 1.0
CG F:LEU362 4.9 13.3 1.0
O F:MET300 5.0 13.8 0.5

Reference:

R.Koralewski, B.Dymek, M.Mazur, P.Sklepkiewicz, S.Olejniczak, W.Czestkowski, K.Matyszewski, G.Andryianau, P.Niedziejko, M.Kowalski, M.Gruza, B.Borek, K.Jedrzejczak, A.Bartoszewicz, E.Pluta, A.Rymaszewska, M.Kania, T.Rejczak, S.Piasecka, M.Mlacki, M.Mazurkiewicz, M.Piotrowicz, M.Salamon, A.Zagozdzon, A.Napiorkowska-Gromadzka, A.Bartlomiejczak, W.Mozga, P.Dobrzanski, K.Dzwonek, J.Golab, M.Nowotny, J.Olczak, A.Golebiowski. Discovery of Oatd-01 , A First-in-Class Chitinase Inhibitor As Potential New Therapeutics For Idiopathic Pulmonary Fibrosis. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33078933
DOI: 10.1021/ACS.JMEDCHEM.0C01179
Page generated: Sat Jul 12 22:21:18 2025

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