Chlorine in PDB 7m41: Structure of Tim-3 in Complex with N-(4-(8-Chloro-2-Methyl-5-Oxo-5,6- Dihydro-[1,2,4]Traizolo[1,5-C]Quinazolin-9-Yl)-3-Methylphenyl)-1H- Imidazole-2-Sulfonamide (Compound 38)

The structure of Structure of Tim-3 in Complex with N-(4-(8-Chloro-2-Methyl-5-Oxo-5,6- Dihydro-[1,2,4]Traizolo[1,5-C]Quinazolin-9-Yl)-3-Methylphenyl)-1H- Imidazole-2-Sulfonamide (Compound 38), PDB code: 7m41 was solved by T.A.Rietz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.91 / 1.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.215, 46.828, 53.905, 90, 93.05, 90
R / Rfree (%)	17 / 21.3

The structure of Structure of Tim-3 in Complex with N-(4-(8-Chloro-2-Methyl-5-Oxo-5,6- Dihydro-[1,2,4]Traizolo[1,5-C]Quinazolin-9-Yl)-3-Methylphenyl)-1H- Imidazole-2-Sulfonamide (Compound 38) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Chlorine atom in the Structure of Tim-3 in Complex with N-(4-(8-Chloro-2-Methyl-5-Oxo-5,6- Dihydro-[1,2,4]Traizolo[1,5-C]Quinazolin-9-Yl)-3-Methylphenyl)-1H- Imidazole-2-Sulfonamide (Compound 38) (pdb code 7m41). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Structure of Tim-3 in Complex with N-(4-(8-Chloro-2-Methyl-5-Oxo-5,6- Dihydro-[1,2,4]Traizolo[1,5-C]Quinazolin-9-Yl)-3-Methylphenyl)-1H- Imidazole-2-Sulfonamide (Compound 38), PDB code: 7m41:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Structure of Tim-3 in Complex with N-(4-(8-Chloro-2-Methyl-5-Oxo-5,6- Dihydro-[1,2,4]Traizolo[1,5-C]Quinazolin-9-Yl)-3-Methylphenyl)-1H- Imidazole-2-Sulfonamide (Compound 38)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Tim-3 in Complex with N-(4-(8-Chloro-2-Methyl-5-Oxo-5,6- Dihydro-[1,2,4]Traizolo[1,5-C]Quinazolin-9-Yl)-3-Methylphenyl)-1H- Imidazole-2-Sulfonamide (Compound 38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:10.7 occ:1.00 CL1 A:YQG201 0.0 10.7 1.0 C3 A:YQG201 1.8 10.9 1.0 C4 A:YQG201 2.7 10.3 1.0 C2 A:YQG201 2.8 8.4 1.0 C11 A:YQG201 3.0 9.4 1.0 C12 A:YQG201 3.3 11.6 1.0 C17 A:YQG201 3.4 14.5 1.0 N A:LEU63 3.5 5.8 1.0 CG2 A:VAL54 3.7 7.9 1.0 C16 A:YQG201 3.8 12.2 1.0 CG1 A:VAL54 3.8 9.9 1.0 CD1 A:LEU47 3.9 10.4 1.0 C5 A:YQG201 3.9 11.2 1.0 C1 A:YQG201 4.0 8.9 1.0 CB A:LEU63 4.1 9.2 1.0 C13 A:YQG201 4.2 12.3 1.0 CB A:VAL54 4.2 9.5 1.0 CA A:LEU63 4.3 8.4 1.0 O A:LEU63 4.3 10.4 1.0 CA A:TRP62 4.3 6.8 1.0 C A:TRP62 4.4 7.1 1.0 CG A:LEU63 4.4 10.5 1.0 C6 A:YQG201 4.5 9.6 1.0 CG A:LEU47 4.6 10.5 1.0 C A:LEU63 4.7 11.4 1.0 C15 A:YQG201 4.7 11.3 1.0 CD2 A:LEU47 4.7 14.1 1.0 CE3 A:TRP62 4.8 10.6 1.0 C14 A:YQG201 4.8 10.3 1.0 CB A:TRP57 4.9 8.0 1.0 O A:TYR61 4.9 8.6 1.0 CD1 A:TRP57 4.9 12.1 1.0

Chlorine binding site 2 out of 2 in the Structure of Tim-3 in Complex with N-(4-(8-Chloro-2-Methyl-5-Oxo-5,6- Dihydro-[1,2,4]Traizolo[1,5-C]Quinazolin-9-Yl)-3-Methylphenyl)-1H- Imidazole-2-Sulfonamide (Compound 38)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Tim-3 in Complex with N-(4-(8-Chloro-2-Methyl-5-Oxo-5,6- Dihydro-[1,2,4]Traizolo[1,5-C]Quinazolin-9-Yl)-3-Methylphenyl)-1H- Imidazole-2-Sulfonamide (Compound 38) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:10.4 occ:1.00 CL1 B:YQG201 0.0 10.4 1.0 C3 B:YQG201 1.8 11.2 1.0 C4 B:YQG201 2.6 11.2 1.0 C2 B:YQG201 2.8 6.0 1.0 C11 B:YQG201 3.0 10.2 1.0 C12 B:YQG201 3.3 11.1 1.0 C17 B:YQG201 3.4 14.7 1.0 N B:LEU63 3.5 6.9 1.0 CG2 B:VAL54 3.7 9.6 1.0 CG1 B:VAL54 3.8 9.5 1.0 C16 B:YQG201 3.8 16.0 1.0 CD1 B:LEU47 3.9 7.4 1.0 C5 B:YQG201 3.9 12.5 1.0 CB B:LEU63 4.0 10.7 1.0 C1 B:YQG201 4.0 10.7 1.0 C13 B:YQG201 4.2 11.1 1.0 CB B:VAL54 4.2 10.5 1.0 O B:LEU63 4.3 11.0 1.0 CA B:LEU63 4.3 8.0 1.0 CA B:TRP62 4.4 8.0 1.0 C B:TRP62 4.4 7.5 1.0 CG B:LEU63 4.4 13.5 1.0 C6 B:YQG201 4.4 10.0 1.0 CG B:LEU47 4.6 9.3 1.0 CD2 B:LEU47 4.6 12.3 1.0 C B:LEU63 4.7 12.4 1.0 C15 B:YQG201 4.7 11.6 1.0 CE3 B:TRP62 4.8 10.7 1.0 C14 B:YQG201 4.8 10.8 1.0 CB B:TRP57 4.8 8.8 1.0 O B:TYR61 4.9 8.9 1.0 CD1 B:TRP57 4.9 13.1 1.0 N1 B:YQG201 5.0 9.8 1.0

T.A.Rietz, K.B.Teuscher, J.J.Mills, R.D.Gogliotti, L.T.Lepovitz, W.R.Scaggs, K.Yoshida, K.Luong, T.Lee, S.W.Fesik. Fragment-Based Discovery of Small Molecules Bound to T-Cell Immunoglobulin and Mucin Domain-Containing Molecule 3 (Tim-3). J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34597046
DOI: 10.1021/ACS.JMEDCHEM.1C01336