Chlorine in PDB 8r5q: Structure of Apo Tdo with A Bound Inhibitor

The structure of Structure of Apo Tdo with A Bound Inhibitor, PDB code: 8r5q was solved by M.Wicki, A.Mac Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.75 / 2.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.33, 132.49, 135.57, 90, 90, 90
R / Rfree (%)	25.4 / 26.7

The binding sites of Chlorine atom in the Structure of Apo Tdo with A Bound Inhibitor (pdb code 8r5q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Structure of Apo Tdo with A Bound Inhibitor, PDB code: 8r5q:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:77.6 occ:1.00 CL1 A:Y5N501 0.0 77.6 1.0 C1 A:Y5N501 1.7 76.0 1.0 C19 A:Y5N501 2.7 75.0 1.0 C2 A:Y5N501 2.7 75.4 1.0 CD2 B:LEU46 3.4 62.7 1.0 CG A:HIS76 3.6 52.4 1.0 CD1 B:LEU46 3.6 62.5 1.0 CG B:LEU46 3.7 62.6 1.0 CB A:HIS76 3.7 51.1 1.0 CD2 B:TYR45 3.7 66.4 1.0 ND1 A:HIS76 3.8 53.7 1.0 CE2 A:PHE72 3.8 57.8 1.0 CE1 B:TYR42 3.8 60.3 1.0 CE2 B:TYR45 3.8 67.1 1.0 CD1 B:TYR42 3.9 60.1 1.0 C5 A:Y5N501 4.0 74.0 1.0 C3 A:Y5N501 4.0 74.9 1.0 CD2 A:HIS76 4.1 53.0 1.0 CD2 A:PHE72 4.1 57.4 1.0 CE1 A:HIS76 4.3 54.0 1.0 O A:PHE72 4.4 58.1 1.0 C4 A:Y5N501 4.5 74.5 1.0 NE2 A:HIS76 4.5 54.2 1.0 CZ A:PHE72 4.6 57.5 1.0 CZ B:TYR42 4.7 61.2 1.0 CG B:TYR42 4.9 60.0 1.0

Chlorine binding site 2 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:68.7 occ:1.00 CL2 A:Y5N501 0.0 68.7 1.0 CE A:Y5N501 1.7 68.5 1.0 NZ A:Y5N501 2.5 69.1 1.0 CD A:Y5N501 2.7 68.2 1.0 CB A:SER155 3.4 68.7 1.0 N A:SER155 3.7 68.9 1.0 N A:GLN154 3.8 74.3 1.0 C17 A:Y5N501 3.8 69.6 1.0 CA A:PHE153 3.9 78.1 1.0 CG A:Y5N501 4.0 68.7 1.0 CD1 A:PHE153 4.0 79.7 1.0 CA A:SER155 4.2 67.7 1.0 CH2 A:TRP324 4.2 57.8 1.0 CB A:PHE153 4.2 77.9 1.0 C A:PHE153 4.2 76.6 1.0 OH B:TYR42 4.4 62.8 1.0 CB A:Y5N501 4.4 69.6 1.0 CB A:PHE158 4.5 64.3 1.0 OG A:SER155 4.5 71.3 1.0 C A:GLN154 4.6 70.6 1.0 CZ3 A:TRP324 4.6 57.4 1.0 CZ B:TYR42 4.6 61.2 1.0 CG A:PHE153 4.6 78.7 1.0 NE2 A:HIS328 4.6 68.4 1.0 CA A:GLN154 4.7 72.2 1.0 CE1 B:TYR42 4.8 60.3 1.0 CD2 A:HIS328 4.8 67.3 1.0 CG A:PHE158 4.9 65.3 1.0 CE2 A:PHE83 5.0 54.2 1.0

Chlorine binding site 3 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl501 b:71.4 occ:1.00 CL1 B:Y5N501 0.0 71.4 1.0 C1 B:Y5N501 1.7 70.3 1.0 C19 B:Y5N501 2.7 69.7 1.0 C2 B:Y5N501 2.7 69.9 1.0 CD2 A:LEU46 3.4 61.6 1.0 CG B:HIS76 3.5 55.9 1.0 CB B:HIS76 3.6 54.6 1.0 ND1 B:HIS76 3.6 57.2 1.0 CD1 A:LEU46 3.6 62.0 1.0 CE2 B:PHE72 3.7 55.0 1.0 CG A:LEU46 3.7 61.7 1.0 CD2 A:TYR45 3.8 66.0 1.0 CE2 A:TYR45 3.9 66.8 1.0 CE1 A:TYR42 3.9 60.0 1.0 C3 B:Y5N501 4.0 69.6 1.0 C5 B:Y5N501 4.0 69.2 1.0 CD2 B:PHE72 4.0 54.1 1.0 CD1 A:TYR42 4.0 59.5 1.0 CD2 B:HIS76 4.1 56.8 1.0 O B:PHE72 4.2 52.6 1.0 CE1 B:HIS76 4.2 58.0 1.0 C4 B:Y5N501 4.5 69.4 1.0 NE2 B:HIS76 4.5 58.2 1.0 CZ B:PHE72 4.6 54.6 1.0 CZ A:TYR42 4.8 60.6 1.0 CG A:TYR42 4.9 59.1 1.0

Chlorine binding site 4 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl501 b:69.7 occ:1.00 CL2 B:Y5N501 0.0 69.7 1.0 CE B:Y5N501 1.7 68.9 1.0 NZ B:Y5N501 2.6 68.7 1.0 CD B:Y5N501 2.7 68.6 1.0 CB B:SER155 3.3 61.3 1.0 N B:SER155 3.7 62.8 1.0 N B:GLN154 3.8 68.8 1.0 C17 B:Y5N501 3.8 68.5 1.0 CA B:PHE153 4.0 72.5 1.0 CG B:Y5N501 4.0 68.3 1.0 CD1 B:PHE153 4.0 73.6 1.0 CH2 B:TRP324 4.1 52.3 1.0 CA B:SER155 4.1 60.8 1.0 CB B:PHE153 4.2 72.0 1.0 C B:PHE153 4.2 70.6 1.0 CB B:PHE158 4.4 54.4 1.0 CB B:Y5N501 4.4 68.2 1.0 CZ3 B:TRP324 4.5 51.9 1.0 OH A:TYR42 4.5 61.3 1.0 OG B:SER155 4.5 63.7 1.0 C B:GLN154 4.5 65.0 1.0 CG B:PHE153 4.6 72.5 1.0 NE2 B:HIS328 4.7 65.0 1.0 CZ A:TYR42 4.7 60.6 1.0 CA B:GLN154 4.7 67.3 1.0 CE1 A:TYR42 4.8 60.0 1.0 CG B:PHE158 4.8 54.7 1.0 CD2 B:HIS328 4.8 64.0 1.0 CD2 B:PHE158 4.9 55.4 1.0 CE2 B:PHE83 5.0 50.7 1.0

Chlorine binding site 5 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl501 b:77.5 occ:1.00 CL1 C:Y5N501 0.0 77.5 1.0 C1 C:Y5N501 1.7 76.3 1.0 C19 C:Y5N501 2.7 75.7 1.0 C2 C:Y5N501 2.7 76.1 1.0 CD2 D:LEU46 3.4 85.2 1.0 CG C:HIS76 3.5 62.5 1.0 CD1 D:LEU46 3.6 85.3 1.0 CG D:LEU46 3.6 84.5 1.0 CB C:HIS76 3.7 61.8 1.0 ND1 C:HIS76 3.7 63.7 1.0 CD2 D:TYR45 3.7 85.1 1.0 CE2 C:PHE72 3.8 65.4 1.0 CE2 D:TYR45 3.9 86.1 1.0 CD1 D:TYR42 3.9 82.0 1.0 CE1 D:TYR42 3.9 82.6 1.0 C3 C:Y5N501 4.0 75.8 1.0 C5 C:Y5N501 4.0 75.1 1.0 CD2 C:HIS76 4.1 62.8 1.0 CD2 C:PHE72 4.1 64.5 1.0 CE1 C:HIS76 4.2 63.8 1.0 O C:PHE72 4.4 64.1 1.0 NE2 C:HIS76 4.5 63.7 1.0 C4 C:Y5N501 4.5 75.5 1.0 CZ C:PHE72 4.6 65.3 1.0 CG D:TYR42 4.8 81.6 1.0 CZ D:TYR42 4.8 83.5 1.0 O D:TYR42 4.9 81.5 1.0 CG D:TYR45 5.0 84.2 1.0

Chlorine binding site 6 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl501 b:72.0 occ:1.00 CL2 C:Y5N501 0.0 72.0 1.0 CE C:Y5N501 1.7 72.0 1.0 NZ C:Y5N501 2.6 71.9 1.0 CD C:Y5N501 2.7 71.8 1.0 CB C:SER155 3.4 76.7 1.0 N C:SER155 3.6 78.0 1.0 N C:GLN154 3.8 83.9 1.0 C17 C:Y5N501 3.9 72.0 1.0 CG C:Y5N501 4.0 71.8 1.0 CA C:PHE153 4.0 86.8 1.0 CD1 C:PHE153 4.0 87.7 1.0 CH2 C:TRP324 4.1 63.3 1.0 CA C:SER155 4.1 75.7 1.0 CB C:PHE153 4.2 86.6 1.0 C C:PHE153 4.2 85.3 1.0 OH D:TYR42 4.4 84.7 1.0 CB C:Y5N501 4.5 72.1 1.0 CB C:PHE158 4.5 63.9 1.0 C C:GLN154 4.5 80.8 1.0 CZ3 C:TRP324 4.5 63.3 1.0 OG C:SER155 4.5 78.3 1.0 CZ D:TYR42 4.6 83.5 1.0 CG C:PHE153 4.6 87.0 1.0 CE1 D:TYR42 4.6 82.6 1.0 NE2 C:HIS328 4.7 70.1 1.0 CA C:GLN154 4.7 82.9 1.0 CD2 C:HIS328 4.8 68.9 1.0 CG C:PHE158 4.8 64.1 1.0 CE2 C:PHE83 5.0 57.3 1.0

Chlorine binding site 7 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl501 b:77.6 occ:1.00 CL1 D:Y5N501 0.0 77.6 1.0 C1 D:Y5N501 1.7 76.5 1.0 C2 D:Y5N501 2.7 76.2 1.0 C19 D:Y5N501 2.7 75.9 1.0 CD2 C:LEU46 3.3 80.2 1.0 CG D:HIS76 3.6 60.9 1.0 CD1 C:LEU46 3.6 80.5 1.0 CG C:LEU46 3.6 79.9 1.0 ND1 D:HIS76 3.7 62.1 1.0 CB D:HIS76 3.7 61.1 1.0 CD2 C:TYR45 3.7 84.5 1.0 CE2 D:PHE72 3.8 64.3 1.0 CE2 C:TYR45 3.8 85.6 1.0 CE1 C:TYR42 3.9 87.9 1.0 C3 D:Y5N501 4.0 76.0 1.0 C5 D:Y5N501 4.0 75.6 1.0 CD1 C:TYR42 4.1 87.0 1.0 CD2 D:PHE72 4.1 63.7 1.0 CD2 D:HIS76 4.1 61.6 1.0 CE1 D:HIS76 4.2 62.5 1.0 O D:PHE72 4.3 64.4 1.0 C4 D:Y5N501 4.5 75.8 1.0 NE2 D:HIS76 4.5 62.5 1.0 CZ D:PHE72 4.7 64.0 1.0 CZ C:TYR42 4.7 88.9 1.0 CG C:TYR42 4.9 85.8 1.0

Chlorine binding site 8 out of 8 in the Structure of Apo Tdo with A Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of Apo Tdo with A Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl501 b:72.4 occ:1.00 CL2 D:Y5N501 0.0 72.4 1.0 CE D:Y5N501 1.8 73.5 1.0 NZ D:Y5N501 2.6 74.0 1.0 CD D:Y5N501 2.7 74.0 1.0 CB D:SER155 3.3 82.2 1.0 N D:SER155 3.7 81.3 1.0 N D:GLN154 3.8 82.4 1.0 C17 D:Y5N501 3.9 74.2 1.0 CG D:Y5N501 4.0 74.1 1.0 CA D:PHE153 4.0 83.6 1.0 CD1 D:PHE153 4.1 83.3 1.0 CH2 D:TRP324 4.1 62.4 1.0 CA D:SER155 4.1 81.0 1.0 CB D:PHE153 4.2 83.1 1.0 OH C:TYR42 4.3 90.5 1.0 C D:PHE153 4.3 83.1 1.0 CB D:Y5N501 4.5 74.4 1.0 CZ3 D:TRP324 4.5 62.6 1.0 OG D:SER155 4.5 84.0 1.0 CB D:PHE158 4.5 74.9 1.0 C D:GLN154 4.5 82.1 1.0 CZ C:TYR42 4.6 88.9 1.0 CG D:PHE153 4.6 82.8 1.0 CE1 C:TYR42 4.7 87.9 1.0 NE2 D:HIS328 4.7 70.1 1.0 CA D:GLN154 4.7 82.5 1.0 CD2 D:HIS328 4.8 68.9 1.0 CG D:PHE158 4.9 75.8 1.0 CE2 D:PHE83 5.0 64.2 1.0

C.Lotz-Jenne, R.Lange, S.Cren, G.Bourquin, L.Goglia, T.Kimmerlin, M.Wicki, M.Mueller, N.Artico, S.Ackerknecht, C.Joesch, A.Mac Sweeney. Discovery and Binding Mode of A Small Molecule Inhibitor of the Apo Form of Human TDO2 Biorxiv 2024.
ISSN: ISSN 2692-8205
DOI: 10.1101/2024.01.09.574827