Zinc 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
Sodium	(Na)	2 atoms

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

Zinc 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 Zinc with other atoms in the Zn 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:Zn301 b:14.3 occ:1.00 NE2 A:HIS232 2.0 15.3 1.0 NE2 A:HIS222 2.1 13.2 1.0 NE2 A:HIS226 2.1 13.4 1.0 O2 A:FMT306 2.1 23.4 1.0 O1 A:FMT306 2.4 19.0 1.0 C A:FMT306 2.5 20.7 1.0 CE1 A:HIS226 3.0 13.5 1.0 CD2 A:HIS232 3.0 15.6 1.0 CE1 A:HIS232 3.0 19.2 1.0 CE1 A:HIS222 3.0 13.8 1.0 CD2 A:HIS222 3.1 11.8 1.0 CD2 A:HIS226 3.1 11.3 1.0 ND1 A:HIS232 4.1 20.4 1.0 CG A:HIS232 4.1 15.6 1.0 O A:HOH433 4.1 28.1 1.0 ND1 A:HIS222 4.1 13.0 1.0 ND1 A:HIS226 4.1 14.5 1.0 CG A:HIS222 4.2 10.7 1.0 CG A:HIS226 4.2 11.8 1.0 O21 A:WLL308 4.5 17.7 1.0 OE2 A:GLU223 4.5 16.6 1.0 O A:HOH488 4.6 15.5 1.0 CE A:MET240 4.7 11.0 1.0 O A:HOH600 4.9 24.6 1.0 OE1 A:GLU223 5.0 16.1 1.0 C22 A:WLL308 5.0 23.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn302 b:14.3 occ:1.00 NE2 A:HIS172 2.0 12.5 1.0 OD2 A:ASP174 2.0 12.8 1.0 NE2 A:HIS187 2.1 13.2 1.0 ND1 A:HIS200 2.1 12.7 1.0 CD2 A:HIS172 2.9 11.6 1.0 CG A:ASP174 2.9 17.1 1.0 CE1 A:HIS187 3.0 15.9 1.0 CE1 A:HIS200 3.0 14.8 1.0 CE1 A:HIS172 3.0 12.0 1.0 CD2 A:HIS187 3.1 11.0 1.0 CG A:HIS200 3.1 12.4 1.0 OD1 A:ASP174 3.2 16.2 1.0 CB A:HIS200 3.5 10.9 1.0 CG A:HIS172 4.1 10.9 1.0 ND1 A:HIS172 4.1 12.8 1.0 ND1 A:HIS187 4.1 15.7 1.0 NE2 A:HIS200 4.2 15.7 1.0 O A:TYR176 4.2 14.6 1.0 CG A:HIS187 4.2 12.2 1.0 CD2 A:HIS200 4.2 11.8 1.0 CB A:ASP174 4.3 13.9 1.0 CE1 A:PHE189 4.5 21.4 1.0 CB A:TYR176 4.6 15.3 1.0 CZ A:PHE189 4.7 23.2 1.0 CE2 A:PHE178 4.8 12.8 1.0 CZ A:PHE178 4.8 13.5 1.0 C A:TYR176 4.9 14.2 1.0 O A:HOH442 4.9 15.8 1.0 CA A:HIS200 5.0 10.2 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn301 b:19.8 occ:1.00 O2 B:FMT306 1.8 39.5 1.0 NE2 B:HIS222 2.0 15.9 1.0 NE2 B:HIS232 2.1 19.3 1.0 NE2 B:HIS226 2.1 20.8 1.0 C B:FMT306 2.5 36.9 1.0 O1 B:FMT306 2.6 38.5 1.0 CD2 B:HIS222 3.0 17.6 1.0 CD2 B:HIS232 3.0 20.9 1.0 CE1 B:HIS222 3.0 19.8 1.0 CD2 B:HIS226 3.1 19.0 1.0 CE1 B:HIS232 3.1 30.1 1.0 CE1 B:HIS226 3.1 19.0 1.0 CG B:HIS222 4.1 14.3 1.0 ND1 B:HIS222 4.1 17.8 1.0 CG B:HIS232 4.1 25.8 1.0 ND1 B:HIS232 4.2 25.9 1.0 ND1 B:HIS226 4.2 20.5 1.0 CG B:HIS226 4.2 17.2 1.0 OE2 B:GLU223 4.5 22.3 1.0 O21 B:WLL308 4.7 24.0 1.0 O B:HOH464 4.7 23.4 1.0 O B:HOH602 4.8 47.4 1.0 CE B:MET240 4.8 17.2 1.0 OE1 B:GLU223 4.8 19.9 1.0 C22 B:WLL308 4.9 33.7 1.0 CD B:GLU223 5.0 20.1 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn302 b:15.9 occ:1.00 OD2 B:ASP174 1.9 17.3 1.0 NE2 B:HIS172 2.0 15.5 1.0 ND1 B:HIS200 2.1 13.8 1.0 NE2 B:HIS187 2.1 14.4 1.0 CG B:ASP174 2.9 21.6 1.0 CD2 B:HIS172 2.9 16.2 1.0 CE1 B:HIS200 3.0 14.4 1.0 CE1 B:HIS172 3.0 13.0 1.0 CE1 B:HIS187 3.0 17.1 1.0 CG B:HIS200 3.1 14.9 1.0 CD2 B:HIS187 3.2 17.6 1.0 OD1 B:ASP174 3.2 17.4 1.0 CB B:HIS200 3.5 14.5 1.0 ND1 B:HIS172 4.1 12.8 1.0 CG B:HIS172 4.1 12.6 1.0 NE2 B:HIS200 4.1 15.5 1.0 ND1 B:HIS187 4.2 16.8 1.0 CD2 B:HIS200 4.2 16.5 1.0 CB B:ASP174 4.3 15.3 1.0 CG B:HIS187 4.3 14.4 1.0 O B:TYR176 4.3 16.2 1.0 CZ B:PHE178 4.6 13.7 1.0 CE2 B:PHE178 4.7 13.6 1.0 CE1 B:PHE189 4.8 20.8 1.0 O B:HOH443 4.8 17.6 1.0 CB B:TYR176 4.8 20.8 1.0 CZ B:PHE189 4.9 19.6 1.0 CA B:HIS200 5.0 13.9 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