Sodium in PDB 3wv3: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide, PDB code: 3wv3 was solved by H.Oki, Y.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.83 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.558, 36.352, 95.853, 90.00, 130.64, 90.00
R / Rfree (%)	16.3 / 21.2

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Zinc	(Zn)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide (pdb code 3wv3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide, PDB code: 3wv3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:25.9 occ:1.00 O A:GLU205 2.6 17.5 1.0 OD2 A:ASP128 2.7 26.6 1.0 OD1 A:ASP203 2.8 19.0 1.0 O A:ASP203 2.9 16.1 1.0 O A:HOH501 3.0 44.2 1.0 OD1 A:ASP128 3.3 30.0 1.0 CG A:ASP128 3.3 23.8 1.0 C A:ASP203 3.6 14.3 1.0 C A:GLU205 3.8 14.5 1.0 OG1 A:THR126 3.8 12.9 1.0 CG A:ASP203 3.8 18.6 1.0 O A:HOH528 3.9 32.4 1.0 CA A:ASP203 4.1 12.9 1.0 CD1 A:TRP207 4.3 12.2 1.0 CD A:PRO127 4.3 13.2 1.0 N A:GLU205 4.4 14.3 1.0 CB A:ASP203 4.4 14.7 1.0 CA A:THR206 4.6 12.6 1.0 N A:ASP204 4.6 10.6 1.0 N A:THR206 4.6 13.0 1.0 C A:ASP204 4.6 13.9 1.0 CB A:ASP128 4.6 16.0 1.0 CA A:GLU205 4.7 12.8 1.0 CA A:ASP204 4.8 11.0 1.0 OD2 A:ASP203 4.8 18.1 1.0 NE1 A:TRP207 4.8 12.3 1.0 CG A:PRO127 4.9 13.6 1.0 N A:TRP207 4.9 11.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]Pyrimidine-2- Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:27.6 occ:1.00 O B:GLU205 2.5 19.1 1.0 OD2 B:ASP128 2.7 25.2 1.0 O B:HOH533 2.7 28.7 1.0 O B:ASP203 2.8 19.1 1.0 OD1 B:ASP203 3.0 18.1 1.0 O B:HOH565 3.2 44.3 1.0 CG B:ASP128 3.4 22.6 1.0 OD1 B:ASP128 3.5 27.3 1.0 C B:ASP203 3.6 16.9 1.0 O B:HOH527 3.7 35.9 1.0 C B:GLU205 3.7 18.8 1.0 OG1 B:THR126 3.9 14.2 1.0 CG B:ASP203 4.0 19.4 1.0 CA B:ASP203 4.2 15.7 1.0 CD1 B:TRP207 4.3 15.3 1.0 N B:GLU205 4.4 18.6 1.0 CD B:PRO127 4.4 15.1 1.0 CA B:THR206 4.4 15.7 1.0 N B:THR206 4.5 16.9 1.0 CB B:ASP203 4.5 16.7 1.0 C B:ASP204 4.6 19.1 1.0 N B:ASP204 4.6 14.8 1.0 CA B:GLU205 4.7 18.2 1.0 CA B:ASP204 4.7 16.9 1.0 CB B:ASP128 4.8 19.4 1.0 N B:TRP207 4.8 16.0 1.0 NE1 B:TRP207 4.9 14.8 1.0 OD2 B:ASP203 4.9 21.0 1.0 CG B:PRO127 5.0 14.0 1.0

H.Nara, K.Sato, T.Naito, H.Mototani, H.Oki, Y.Yamamoto, H.Kuno, T.Santou, N.Kanzaki, J.Terauchi, O.Uchikawa, M.Kori. Thieno[2,3-D]Pyrimidine-2-Carboxamides Bearing A Carboxybenzene Group at 5-Position: Highly Potent, Selective, and Orally Available Mmp-13 Inhibitors Interacting with the S1 Binding Site Bioorg.Med.Chem. 2014.
ISSN: ESSN 1464-3391
PubMed: 25192810
DOI: 10.1016/J.BMC.2014.07.025