Calcium 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:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca202 b:56.3 occ:1.00 OD1 A:ASP99 2.4 19.9 1.0 O A:ILE96 2.5 56.0 1.0 O A:ILE93 2.5 27.1 1.0 C A:ILE96 3.3 61.4 1.0 OD1 A:ASN98 3.5 41.5 1.0 CG A:ASP99 3.5 21.5 1.0 C A:MET97 3.7 55.6 1.0 N A:ASN98 3.7 52.9 1.0 C A:ILE93 3.7 23.0 1.0 CA A:MET97 3.8 58.9 1.0 N A:ASP99 3.9 23.9 1.0 N A:MET97 3.9 59.1 1.0 O A:MET97 4.1 51.5 1.0 N A:ILE96 4.2 51.6 1.0 OD2 A:ASP99 4.2 19.3 1.0 C A:ASN98 4.2 23.8 1.0 CA A:ILE96 4.3 53.9 1.0 N A:ILE93 4.3 20.2 1.0 CA A:ILE93 4.4 18.6 1.0 CA A:ASP99 4.4 22.5 1.0 CB A:ASP99 4.5 18.8 1.0 CA A:ASN98 4.5 36.1 1.0 CB A:ILE93 4.5 22.5 1.0 CG A:ASN98 4.6 42.7 1.0 N A:PRO94 4.7 23.2 1.0 CA A:PRO94 4.8 30.9 1.0 O A:ASN98 4.9 24.8 1.0 C A:PRO94 4.9 30.9 1.0 C A:GLN92 4.9 16.0 1.0 N A:GLY95 5.0 34.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca202 b:18.6 occ:1.00 O B:ILE93 2.2 15.7 1.0 OD1 B:ASP99 2.3 11.8 1.0 OD1 B:ASN98 2.3 21.4 1.0 O B:HOH399 2.4 23.6 1.0 O B:GLY95 2.4 21.9 1.0 CG B:ASP99 3.3 16.1 1.0 C B:GLY95 3.4 24.6 1.0 C B:ILE93 3.5 16.1 1.0 CG B:ASN98 3.5 23.1 1.0 N B:ASP99 3.8 19.9 1.0 N B:GLY95 4.0 19.0 1.0 OD2 B:ASP99 4.0 17.6 1.0 C B:PRO94 4.1 15.6 1.0 N B:ILE93 4.1 12.6 1.0 ND2 B:ASN98 4.2 17.6 1.0 CA B:GLY95 4.2 16.9 1.0 C B:ASN98 4.2 14.0 1.0 N B:ASN98 4.3 19.6 1.0 CA B:ILE93 4.3 11.3 1.0 N B:ILE96 4.3 21.2 1.0 CA B:ASP99 4.3 17.8 1.0 CB B:ASP99 4.4 16.1 1.0 N B:PRO94 4.4 14.1 1.0 CA B:PRO94 4.4 18.1 1.0 O B:PRO94 4.5 12.5 1.0 C B:GLN92 4.6 13.6 1.0 CA B:ILE96 4.6 28.6 1.0 O B:HOH328 4.6 25.4 1.0 CA B:ASN98 4.6 21.7 1.0 CB B:ILE93 4.6 18.0 1.0 CB B:ASN98 4.6 21.3 1.0 O B:HOH403 4.6 30.8 1.0 C B:ILE96 4.7 23.4 1.0 N B:MET97 4.8 26.6 1.0 O B:ASN98 4.8 15.4 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