Zinc in PDB 5b5p: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide, PDB code: 5b5p 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)	36.84 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.798, 36.281, 96.382, 90.00, 130.14, 90.00
R / Rfree (%)	17.3 / 20.8

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide (pdb code 5b5p). 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 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide, PDB code: 5b5p:
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 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-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 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.6 occ:1.00 N30 A:WNN306 1.6 14.9 1.0 NE2 A:HIS222 2.0 13.8 1.0 NE2 A:HIS232 2.1 19.7 1.0 NE2 A:HIS226 2.1 14.1 1.0 N29 A:WNN306 2.6 25.0 1.0 C26 A:WNN306 2.7 26.9 1.0 CD2 A:HIS222 2.9 16.5 1.0 CD2 A:HIS232 3.0 20.2 1.0 CE1 A:HIS222 3.0 16.7 1.0 CE1 A:HIS226 3.1 20.3 1.0 CE1 A:HIS232 3.1 26.0 1.0 CD2 A:HIS226 3.1 17.8 1.0 S25 A:WNN306 3.4 30.0 1.0 C28 A:WNN306 3.8 26.1 1.0 N27 A:WNN306 3.8 30.5 1.0 ND1 A:HIS222 4.1 18.4 1.0 CG A:HIS222 4.1 14.1 1.0 CG A:HIS232 4.1 20.4 1.0 ND1 A:HIS232 4.1 23.4 1.0 ND1 A:HIS226 4.2 16.8 1.0 CG A:HIS226 4.2 14.2 1.0 OE2 A:GLU223 4.3 22.9 1.0 C23 A:WNN306 4.6 26.6 1.0 C24 A:WNN306 4.7 31.8 1.0 O A:HOH526 4.7 20.7 1.0 CE A:MET240 4.7 15.2 1.0 O22 A:WNN306 4.9 26.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-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 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:17.8 occ:1.00 NE2 A:HIS172 1.8 14.0 1.0 OD2 A:ASP174 1.9 18.8 1.0 NE2 A:HIS187 2.1 21.5 1.0 ND1 A:HIS200 2.1 18.7 1.0 CD2 A:HIS172 2.8 18.0 1.0 CE1 A:HIS172 2.8 17.3 1.0 CG A:ASP174 2.9 20.4 1.0 CE1 A:HIS187 2.9 24.9 1.0 CE1 A:HIS200 3.0 20.3 1.0 OD1 A:ASP174 3.1 18.4 1.0 CD2 A:HIS187 3.1 21.5 1.0 CG A:HIS200 3.2 17.8 1.0 CB A:HIS200 3.5 17.3 1.0 ND1 A:HIS172 3.9 16.8 1.0 CG A:HIS172 3.9 14.2 1.0 ND1 A:HIS187 4.1 26.6 1.0 O A:TYR176 4.1 18.9 1.0 NE2 A:HIS200 4.2 22.4 1.0 CG A:HIS187 4.2 18.4 1.0 CB A:ASP174 4.3 19.2 1.0 CD2 A:HIS200 4.3 17.1 1.0 CE1 A:PHE189 4.6 26.2 1.0 CB A:TYR176 4.6 23.9 1.0 CZ A:PHE189 4.8 27.5 1.0 CZ A:PHE178 4.8 18.7 1.0 CE2 A:PHE178 4.8 18.4 1.0 C A:TYR176 4.9 19.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-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 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:18.9 occ:1.00 N30 B:WNN306 1.5 11.8 1.0 NE2 B:HIS232 2.0 21.2 1.0 NE2 B:HIS222 2.1 17.1 1.0 NE2 B:HIS226 2.1 25.4 1.0 N29 B:WNN306 2.5 27.1 1.0 C26 B:WNN306 2.7 23.2 1.0 CD2 B:HIS232 2.9 20.5 1.0 CD2 B:HIS222 2.9 22.1 1.0 CE1 B:HIS226 3.1 23.0 1.0 CD2 B:HIS226 3.1 23.3 1.0 CE1 B:HIS232 3.1 26.4 1.0 CE1 B:HIS222 3.1 18.4 1.0 S25 B:WNN306 3.5 27.0 1.0 C28 B:WNN306 3.7 19.0 1.0 N27 B:WNN306 3.8 28.5 1.0 CG B:HIS232 4.1 23.6 1.0 CG B:HIS222 4.1 16.3 1.0 ND1 B:HIS232 4.1 23.9 1.0 ND1 B:HIS226 4.2 22.1 1.0 ND1 B:HIS222 4.2 16.7 1.0 CG B:HIS226 4.2 19.8 1.0 OE2 B:GLU223 4.3 26.9 1.0 C23 B:WNN306 4.4 32.3 1.0 C24 B:WNN306 4.7 29.5 1.0 O B:HOH560 4.7 47.3 1.0 CE B:MET240 4.7 20.5 1.0 O B:HOH531 4.8 22.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-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 4- Oxo-N-(3-(2-(1H-1,2,4-Triazol-3-Ylsulfanyl)Ethoxy)Benzyl)-3,4- Dihydroquinazoline-2-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:17.8 occ:1.00 NE2 B:HIS172 1.8 12.7 1.0 OD2 B:ASP174 2.0 19.6 1.0 NE2 B:HIS187 2.1 17.9 1.0 ND1 B:HIS200 2.1 15.9 1.0 CE1 B:HIS172 2.8 18.2 1.0 CD2 B:HIS172 2.9 17.2 1.0 CG B:ASP174 2.9 23.9 1.0 CE1 B:HIS187 3.0 18.7 1.0 CE1 B:HIS200 3.0 17.3 1.0 CD2 B:HIS187 3.1 19.7 1.0 CG B:HIS200 3.2 16.2 1.0 OD1 B:ASP174 3.2 21.9 1.0 CB B:HIS200 3.5 16.8 1.0 ND1 B:HIS172 3.9 18.4 1.0 CG B:HIS172 4.0 14.7 1.0 ND1 B:HIS187 4.1 18.1 1.0 NE2 B:HIS200 4.1 18.0 1.0 CG B:HIS187 4.2 18.4 1.0 CD2 B:HIS200 4.2 18.6 1.0 CB B:ASP174 4.3 20.2 1.0 O B:TYR176 4.3 20.4 1.0 CZ B:PHE178 4.6 18.9 1.0 CE1 B:PHE189 4.7 24.3 1.0 O B:HOH452 4.7 19.9 1.0 CE2 B:PHE178 4.7 20.7 1.0 CB B:TYR176 4.8 24.0 1.0 CZ B:PHE189 4.9 26.5 1.0

H.Nara, A.Kaieda, K.Sato, T.Naito, H.Mototani, H.Oki, Y.Yamamoto, H.Kuno, T.Santou, N.Kanzaki, J.Terauchi, O.Uchikawa, M.Kori. Discovery of Novel, Highly Potent, and Selective Matrix Metalloproteinase (Mmp)-13 Inhibitors with A 1,2,4-Triazol-3-Yl Moiety As A Zinc Binding Group Using A Structure-Based Design Approach J. Med. Chem. V. 60 608 2017.
ISSN: ISSN 1520-4804
PubMed: 27966948
DOI: 10.1021/ACS.JMEDCHEM.6B01007