Sodium in PDB 3wv2: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide, PDB code: 3wv2 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)	19.91 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.530, 35.719, 94.762, 90.00, 135.29, 90.00
R / Rfree (%)	17.1 / 24.1

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- (3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-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-Dihydroquinazoline-2-Carboxamide (pdb code 3wv2). 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-Dihydroquinazoline-2-Carboxamide, PDB code: 3wv2:
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-Dihydroquinazoline-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-Dihydroquinazoline-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:14.8 occ:1.00 OD2 A:ASP128 2.2 19.5 1.0 O A:GLU205 2.4 17.4 1.0 OD1 A:ASP203 2.5 15.3 1.0 O A:ASP203 2.7 18.4 1.0 CG A:ASP128 3.2 21.3 1.0 OD1 A:ASP128 3.4 30.4 1.0 C A:ASP203 3.4 17.1 1.0 O A:HOH699 3.4 28.6 1.0 C A:GLU205 3.6 17.1 1.0 CG A:ASP203 3.6 16.8 1.0 OG1 A:THR126 3.7 12.2 1.0 CA A:ASP203 3.9 14.6 1.0 CB A:ASP203 4.2 15.7 1.0 CD1 A:TRP207 4.2 14.6 1.0 N A:GLU205 4.3 16.6 1.0 N A:THR206 4.4 19.3 1.0 N A:ASP204 4.4 16.8 1.0 CD A:PRO127 4.4 13.2 1.0 CA A:THR206 4.4 20.4 1.0 C A:ASP204 4.4 18.6 1.0 CB A:ASP128 4.5 18.6 1.0 CA A:GLU205 4.6 16.6 1.0 OD2 A:ASP203 4.6 17.4 1.0 CA A:ASP204 4.6 18.3 1.0 N A:TRP207 4.7 17.8 1.0 NE1 A:TRP207 4.8 14.4 1.0 CG A:PRO127 5.0 13.8 1.0 O A:ASP204 5.0 20.9 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-Dihydroquinazoline-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-Dihydroquinazoline-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:14.4 occ:1.00 O B:ASP203 2.3 22.6 1.0 O B:HOH476 2.4 26.2 1.0 OD2 B:ASP128 2.4 21.0 1.0 O B:GLU205 2.4 22.2 1.0 OD1 B:ASP203 2.6 23.8 1.0 O B:HOH486 2.6 30.0 1.0 OD1 B:ASP128 2.9 21.3 1.0 CG B:ASP128 3.0 20.2 1.0 C B:ASP203 3.3 20.2 1.0 C B:GLU205 3.6 20.4 1.0 CG B:ASP203 3.6 22.2 1.0 O B:HOH471 3.7 25.1 1.0 OG1 B:THR126 3.8 18.3 1.0 CA B:ASP203 3.9 20.7 1.0 CB B:ASP203 4.2 21.1 1.0 CA B:THR206 4.2 20.4 1.0 N B:THR206 4.3 20.6 1.0 CD1 B:TRP207 4.4 19.1 1.0 N B:GLU205 4.4 21.1 1.0 N B:ASP204 4.4 20.1 1.0 CB B:ASP128 4.5 19.4 1.0 C B:ASP204 4.5 22.0 1.0 CA B:GLU205 4.6 21.8 1.0 CD B:PRO127 4.6 16.6 1.0 OD2 B:ASP203 4.7 23.1 1.0 CA B:ASP204 4.7 21.5 1.0 N B:TRP207 4.7 21.2 1.0 NE1 B:TRP207 4.9 18.8 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