Zinc 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
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-Dihydroquinazoline-2-Carboxamide (pdb code 3wv2). 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-Dihydroquinazoline-2-Carboxamide, PDB code: 3wv2:
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-Dihydroquinazoline-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-Dihydroquinazoline-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.1 occ:1.00 NE2 A:HIS226 2.0 13.8 1.0 NE2 A:HIS232 2.0 16.2 1.0 NE2 A:HIS222 2.1 12.4 1.0 O A:HOH602 2.4 17.2 1.0 CD2 A:HIS232 2.9 15.9 1.0 CD2 A:HIS222 3.0 12.2 1.0 CE1 A:HIS226 3.0 14.5 1.0 CD2 A:HIS226 3.0 13.4 1.0 CE1 A:HIS232 3.1 16.8 1.0 CE1 A:HIS222 3.1 13.3 1.0 CG A:HIS232 4.1 16.2 1.0 ND1 A:HIS226 4.1 13.2 1.0 ND1 A:HIS232 4.1 17.3 1.0 CG A:HIS226 4.2 14.2 1.0 CG A:HIS222 4.2 13.3 1.0 ND1 A:HIS222 4.2 12.6 1.0 O A:HOH706 4.3 31.1 1.0 O A:HOH714 4.4 22.4 1.0 OE2 A:GLU223 4.5 18.3 1.0 O9 A:WGG306 4.5 21.4 1.0 CE A:MET240 4.6 12.7 1.0 C10 A:WGG306 4.7 21.1 1.0 OE1 A:GLU223 4.9 17.8 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-Dihydroquinazoline-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-Dihydroquinazoline-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:16.2 occ:1.00 OD2 A:ASP174 1.9 19.9 1.0 NE2 A:HIS172 1.9 14.4 1.0 NE2 A:HIS187 2.0 16.5 1.0 ND1 A:HIS200 2.1 16.5 1.0 CG A:ASP174 2.8 18.8 1.0 CD2 A:HIS172 2.8 14.4 1.0 CE1 A:HIS187 2.8 16.7 1.0 CG A:HIS200 3.0 16.0 1.0 CE1 A:HIS172 3.0 16.0 1.0 OD1 A:ASP174 3.1 17.7 1.0 CE1 A:HIS200 3.1 17.5 1.0 CD2 A:HIS187 3.2 16.0 1.0 CB A:HIS200 3.3 14.7 1.0 CG A:HIS172 4.0 14.6 1.0 ND1 A:HIS187 4.0 17.1 1.0 ND1 A:HIS172 4.1 15.0 1.0 O A:TYR176 4.1 18.3 1.0 CD2 A:HIS200 4.2 16.0 1.0 NE2 A:HIS200 4.2 15.8 1.0 CB A:ASP174 4.2 19.0 1.0 CG A:HIS187 4.2 16.8 1.0 CE1 A:PHE189 4.5 26.1 1.0 CZ A:PHE178 4.6 15.4 1.0 CB A:TYR176 4.6 25.7 1.0 CE2 A:PHE178 4.6 14.5 1.0 CZ A:PHE189 4.8 29.3 1.0 CA A:HIS200 4.8 14.0 1.0 O A:HOH601 4.8 17.8 1.0 C A:TYR176 4.9 21.4 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-Dihydroquinazoline-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-Dihydroquinazoline-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:30.1 occ:1.00 NE2 B:HIS226 2.0 29.2 1.0 NE2 B:HIS232 2.1 44.0 1.0 NE2 B:HIS222 2.1 27.5 1.0 O B:HOH473 2.4 21.4 1.0 CD2 B:HIS232 2.9 40.0 1.0 CD2 B:HIS222 2.9 26.7 1.0 CD2 B:HIS226 2.9 27.6 1.0 CE1 B:HIS226 3.0 31.4 1.0 CE1 B:HIS232 3.1 46.8 1.0 CE1 B:HIS222 3.3 27.9 1.0 CG B:HIS232 4.0 38.9 1.0 ND1 B:HIS232 4.1 44.2 1.0 ND1 B:HIS226 4.1 29.3 1.0 CG B:HIS226 4.1 27.6 1.0 CG B:HIS222 4.1 27.3 1.0 ND1 B:HIS222 4.3 28.2 1.0 OE1 B:GLU223 4.4 26.9 1.0 OE2 B:GLU223 4.4 29.1 1.0 C10 B:WGG306 4.6 50.5 1.0 CE B:MET240 4.6 24.4 1.0 CD B:GLU223 4.7 25.1 1.0 O B:HOH402 4.9 31.8 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-Dihydroquinazoline-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-Dihydroquinazoline-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:22.5 occ:1.00 OD2 B:ASP174 1.9 24.9 1.0 NE2 B:HIS172 2.0 17.6 1.0 NE2 B:HIS187 2.1 17.8 1.0 ND1 B:HIS200 2.1 19.5 1.0 CD2 B:HIS172 2.8 17.6 1.0 CG B:ASP174 2.9 24.9 1.0 CE1 B:HIS187 3.0 18.5 1.0 CE1 B:HIS200 3.0 19.3 1.0 CE1 B:HIS172 3.0 18.3 1.0 CG B:HIS200 3.1 18.5 1.0 CD2 B:HIS187 3.1 19.8 1.0 OD1 B:ASP174 3.1 23.6 1.0 CB B:HIS200 3.5 18.3 1.0 CG B:HIS172 4.0 17.7 1.0 ND1 B:HIS172 4.1 17.6 1.0 ND1 B:HIS187 4.1 20.0 1.0 NE2 B:HIS200 4.1 18.8 1.0 CD2 B:HIS200 4.2 19.5 1.0 O B:TYR176 4.2 22.3 1.0 CG B:HIS187 4.2 20.2 1.0 CB B:ASP174 4.2 22.9 1.0 CZ B:PHE178 4.5 20.1 1.0 CE2 B:PHE178 4.6 21.2 1.0 CE1 B:PHE189 4.7 28.6 1.0 CZ B:PHE189 4.7 30.5 1.0 O B:HOH466 4.8 16.2 1.0 CB B:TYR176 4.9 27.7 1.0 CA B:HIS200 4.9 17.3 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