Calcium 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:

Zinc	(Zn)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca303 b:14.2 occ:1.00 OE2 A:GLU205 2.2 20.1 1.0 O A:GLY180 2.3 15.5 1.0 OD2 A:ASP202 2.3 13.0 1.0 OD1 A:ASP179 2.3 15.2 1.0 O A:SER182 2.3 19.0 1.0 O A:LEU184 2.3 14.9 1.0 CG A:ASP202 3.4 11.9 1.0 C A:SER182 3.5 23.0 1.0 CG A:ASP179 3.5 20.6 1.0 CD A:GLU205 3.5 20.3 1.0 C A:GLY180 3.5 16.0 1.0 C A:LEU184 3.5 15.7 1.0 N A:SER182 3.9 21.9 1.0 N A:LEU184 3.9 17.1 1.0 C A:PRO181 4.0 21.6 1.0 OD2 A:ASP179 4.0 20.9 1.0 N A:GLY180 4.2 15.7 1.0 CA A:LEU184 4.2 16.3 1.0 C A:GLY183 4.2 19.0 1.0 CB A:ASP202 4.2 11.0 1.0 CA A:SER182 4.2 24.3 1.0 CG A:GLU205 4.3 14.7 1.0 OD1 A:ASP202 4.3 11.1 1.0 C A:ASP179 4.3 16.4 1.0 N A:ASP179 4.3 15.4 1.0 CA A:PRO181 4.4 20.0 1.0 OE1 A:GLU205 4.4 18.8 1.0 N A:PRO181 4.4 18.9 1.0 O A:PRO181 4.4 23.5 1.0 N A:GLY183 4.4 19.9 1.0 CA A:GLY180 4.4 15.8 1.0 CA A:GLY183 4.5 18.9 1.0 CB A:LEU184 4.6 20.0 1.0 N A:LEU185 4.6 13.9 1.0 CA A:ASP179 4.6 17.4 1.0 CB A:ASP179 4.6 17.6 1.0 O A:ASP179 4.7 16.2 1.0 O A:GLY183 4.7 19.1 1.0 O A:HOH539 4.9 32.5 1.0 CA A:LEU185 4.9 14.7 1.0

Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca 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 A:Ca304 b:16.1 occ:1.00 O A:GLY196 2.3 15.0 1.0 O A:ASN194 2.3 21.6 1.0 O A:HOH409 2.3 15.6 1.0 O A:ASP162 2.4 15.2 1.0 O A:HOH416 2.4 15.1 1.0 OD1 A:ASP198 2.4 12.0 1.0 CG A:ASP198 3.4 16.3 1.0 C A:GLY196 3.5 15.1 1.0 C A:ASP162 3.5 12.4 1.0 C A:ASN194 3.6 20.4 1.0 C A:TYR195 3.9 16.7 1.0 OD2 A:ASP198 3.9 17.1 1.0 N A:GLY196 3.9 17.1 1.0 O A:TYR195 4.1 14.9 1.0 O A:ALA161 4.2 14.9 1.0 N A:ASP198 4.2 11.8 1.0 O A:HOH589 4.2 50.1 1.0 CA A:GLY196 4.2 14.4 1.0 O A:HOH474 4.3 22.3 1.0 CA A:ASP162 4.3 13.9 1.0 CA A:TYR195 4.3 19.5 1.0 N A:TYR195 4.4 20.3 1.0 O A:GLY192 4.4 18.5 1.0 N A:GLY197 4.5 13.6 1.0 CA A:ASN194 4.5 23.2 1.0 N A:ILE163 4.5 11.3 1.0 N A:ASN194 4.6 23.1 1.0 CB A:ASP198 4.6 13.1 1.0 CA A:GLY197 4.6 13.0 1.0 C A:GLY197 4.7 12.8 1.0 O A:HOH427 4.7 17.5 1.0 N A:MET164 4.7 12.4 1.0 CA A:ILE163 4.7 11.4 1.0 CA A:ASP198 4.8 12.6 1.0 CG A:MET164 4.8 14.3 1.0 C A:PRO193 4.8 21.7 1.0 CH2 A:TRP113 4.9 20.1 1.0

Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca binding site number 3 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:Ca303 b:18.8 occ:1.00 OE2 B:GLU205 2.2 23.3 1.0 O B:GLY180 2.2 21.9 1.0 O B:LEU184 2.3 18.2 1.0 OD2 B:ASP202 2.3 15.7 1.0 O B:SER182 2.3 24.8 1.0 OD1 B:ASP179 2.4 20.3 1.0 CG B:ASP202 3.4 17.1 1.0 C B:LEU184 3.4 17.5 1.0 CD B:GLU205 3.5 19.1 1.0 C B:GLY180 3.5 21.9 1.0 C B:SER182 3.5 26.7 1.0 CG B:ASP179 3.6 21.7 1.0 N B:LEU184 3.9 20.8 1.0 N B:SER182 3.9 27.2 1.0 C B:PRO181 4.0 26.4 1.0 N B:GLY180 4.1 22.0 1.0 CB B:ASP202 4.1 16.0 1.0 OD2 B:ASP179 4.1 24.2 1.0 CA B:LEU184 4.2 19.3 1.0 CA B:SER182 4.2 27.8 1.0 C B:GLY183 4.3 21.8 1.0 OE1 B:GLU205 4.3 21.0 1.0 N B:ASP179 4.3 21.9 1.0 C B:ASP179 4.3 22.7 1.0 OD1 B:ASP202 4.3 15.3 1.0 CA B:GLY180 4.4 22.1 1.0 CG B:GLU205 4.4 22.4 1.0 N B:PRO181 4.4 23.8 1.0 O B:PRO181 4.4 26.9 1.0 CA B:PRO181 4.4 25.2 1.0 N B:LEU185 4.5 17.7 1.0 N B:GLY183 4.5 23.4 1.0 CB B:LEU184 4.5 17.9 1.0 CA B:ASP179 4.6 22.5 1.0 CA B:GLY183 4.7 22.7 1.0 CB B:ASP179 4.7 22.8 1.0 CA B:LEU185 4.7 17.2 1.0 O B:GLY183 4.8 23.3 1.0 O B:ASP179 4.8 23.6 1.0

Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca binding site number 4 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:Ca304 b:15.9 occ:1.00 O B:GLY196 2.3 17.2 1.0 O B:ASN194 2.3 18.8 1.0 O B:ASP162 2.3 14.7 1.0 O B:HOH423 2.4 16.8 1.0 O B:HOH449 2.4 20.2 1.0 OD1 B:ASP198 2.4 16.3 1.0 CG B:ASP198 3.4 16.2 1.0 C B:GLY196 3.5 14.2 1.0 C B:ASP162 3.5 13.3 1.0 C B:ASN194 3.5 21.2 1.0 C B:TYR195 3.9 17.0 1.0 OD2 B:ASP198 3.9 17.6 1.0 N B:GLY196 4.0 17.1 1.0 O B:TYR195 4.0 18.1 1.0 O B:ALA161 4.1 16.8 1.0 O B:HOH500 4.1 23.8 1.0 N B:ASP198 4.1 14.9 1.0 CA B:ASP162 4.2 14.2 1.0 O B:HOH498 4.3 45.8 1.0 CA B:GLY196 4.3 15.9 1.0 N B:TYR195 4.4 18.4 1.0 CA B:TYR195 4.4 18.5 1.0 N B:ASN194 4.4 22.5 1.0 CA B:ASN194 4.4 23.2 1.0 O B:GLY192 4.4 20.6 1.0 N B:GLY197 4.4 15.2 1.0 N B:ILE163 4.5 12.5 1.0 CA B:GLY197 4.6 13.5 1.0 CB B:ASP198 4.6 14.4 1.0 C B:GLY197 4.6 15.4 1.0 N B:MET164 4.7 11.9 1.0 CA B:ILE163 4.7 14.1 1.0 CA B:ASP198 4.7 13.6 1.0 O B:HOH439 4.7 18.1 1.0 C B:PRO193 4.8 23.3 1.0 CG B:MET164 4.9 14.0 1.0 O B:PRO193 5.0 23.4 1.0 CH2 B:TRP113 5.0 17.8 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