Zinc in PDB 5b5o: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine, PDB code: 5b5o 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)	33.75 / 1.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.409, 36.060, 95.948, 90.00, 131.09, 90.00
R / Rfree (%)	16.4 / 18.5

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine 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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine (pdb code 5b5o). 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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine, PDB code: 5b5o:
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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.1 occ:1.00 N12 A:WMM307 1.9 18.9 1.0 NE2 A:HIS232 2.0 9.0 1.0 NE2 A:HIS222 2.0 7.9 1.0 NE2 A:HIS226 2.1 8.2 1.0 N11 A:WMM307 2.9 15.9 1.0 C8 A:WMM307 3.0 20.8 1.0 CD2 A:HIS232 3.0 9.3 1.0 CE1 A:HIS222 3.0 8.0 1.0 CE1 A:HIS232 3.0 11.3 1.0 CD2 A:HIS222 3.0 8.6 1.0 CE1 A:HIS226 3.1 8.1 1.0 CD2 A:HIS226 3.1 7.7 1.0 S7 A:WMM307 3.6 22.8 1.0 C10 A:WMM307 4.0 19.8 1.0 N9 A:WMM307 4.1 19.5 1.0 ND1 A:HIS232 4.1 11.4 1.0 CG A:HIS232 4.1 8.7 1.0 ND1 A:HIS222 4.1 7.2 1.0 CG A:HIS222 4.2 6.9 1.0 ND1 A:HIS226 4.2 8.7 1.0 CG A:HIS226 4.2 7.2 1.0 OE2 A:GLU223 4.3 11.0 1.0 O A:HOH568 4.5 16.5 1.0 N2 A:WMM307 4.6 22.3 1.0 OE1 A:GLU223 4.6 10.1 1.0 C3 A:WMM307 4.6 25.8 1.0 C6 A:WMM307 4.7 24.7 1.0 CD A:GLU223 4.8 8.3 1.0 CE A:MET240 4.8 8.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.0 occ:1.00 OD2 A:ASP174 1.9 10.2 1.0 NE2 A:HIS172 2.0 8.1 1.0 ND1 A:HIS200 2.1 7.4 1.0 NE2 A:HIS187 2.1 11.4 1.0 CG A:ASP174 2.9 9.1 1.0 CD2 A:HIS172 3.0 8.0 1.0 CE1 A:HIS200 3.0 9.8 1.0 CE1 A:HIS187 3.0 14.1 1.0 CE1 A:HIS172 3.0 8.4 1.0 CG A:HIS200 3.1 7.3 1.0 CD2 A:HIS187 3.1 11.2 1.0 OD1 A:ASP174 3.1 9.2 1.0 CB A:HIS200 3.5 7.9 1.0 O A:TYR176 4.1 10.6 1.0 CG A:HIS172 4.1 7.6 1.0 ND1 A:HIS172 4.1 8.2 1.0 NE2 A:HIS200 4.1 9.0 1.0 ND1 A:HIS187 4.2 13.2 1.0 CD2 A:HIS200 4.2 8.4 1.0 CG A:HIS187 4.2 10.5 1.0 CB A:ASP174 4.3 10.9 1.0 CE1 A:PHE189 4.5 15.1 1.0 CZ A:PHE189 4.6 17.5 1.0 CB A:TYR176 4.6 11.8 1.0 CE2 A:PHE178 4.8 8.9 1.0 CZ A:PHE178 4.8 10.0 1.0 C A:TYR176 4.9 10.8 1.0 O A:HOH506 4.9 10.1 1.0 CA A:HIS200 5.0 6.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:9.9 occ:1.00 N12 B:WMM306 2.0 12.6 1.0 NE2 B:HIS232 2.0 10.1 1.0 NE2 B:HIS222 2.0 9.3 1.0 NE2 B:HIS226 2.1 9.3 1.0 C8 B:WMM306 2.9 13.3 1.0 N11 B:WMM306 2.9 14.1 1.0 CD2 B:HIS232 3.0 10.0 1.0 CD2 B:HIS222 3.0 9.5 1.0 CE1 B:HIS232 3.0 12.5 1.0 CE1 B:HIS226 3.0 10.0 1.0 CE1 B:HIS222 3.1 9.6 1.0 CD2 B:HIS226 3.1 8.8 1.0 S7 B:WMM306 3.5 18.7 1.0 C10 B:WMM306 4.0 16.0 1.0 N9 B:WMM306 4.1 17.5 1.0 ND1 B:HIS232 4.1 11.9 1.0 CG B:HIS232 4.1 10.7 1.0 CG B:HIS222 4.1 9.3 1.0 ND1 B:HIS222 4.2 9.4 1.0 ND1 B:HIS226 4.2 10.4 1.0 OE2 B:GLU223 4.2 16.2 1.0 CG B:HIS226 4.2 9.3 1.0 N2 B:WMM306 4.6 19.2 1.0 C3 B:WMM306 4.6 17.1 1.0 O B:HOH549 4.7 31.1 1.0 O B:HOH552 4.7 13.5 1.0 CE B:MET240 4.7 10.8 1.0 C6 B:WMM306 4.8 20.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with N- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine


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- Phenyl-4-((4H-1,2,4-Triazol-3-Ylsulfanyl)Methyl)-1,3-Thiazol-2-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:8.1 occ:1.00 OD2 B:ASP174 2.0 9.2 1.0 NE2 B:HIS172 2.0 7.9 1.0 NE2 B:HIS187 2.0 7.9 1.0 ND1 B:HIS200 2.0 7.1 1.0 CG B:ASP174 2.9 8.5 1.0 CE1 B:HIS200 2.9 8.3 1.0 CE1 B:HIS187 3.0 10.1 1.0 CD2 B:HIS172 3.0 8.0 1.0 CE1 B:HIS172 3.0 7.4 1.0 CD2 B:HIS187 3.1 8.8 1.0 CG B:HIS200 3.1 6.8 1.0 OD1 B:ASP174 3.2 8.8 1.0 CB B:HIS200 3.5 8.6 1.0 NE2 B:HIS200 4.1 8.2 1.0 ND1 B:HIS187 4.1 9.7 1.0 ND1 B:HIS172 4.1 7.8 1.0 CG B:HIS172 4.1 8.2 1.0 CG B:HIS187 4.2 8.2 1.0 CD2 B:HIS200 4.2 8.1 1.0 CB B:ASP174 4.2 9.6 1.0 O B:TYR176 4.4 10.1 1.0 CZ B:PHE178 4.7 9.4 1.0 CE1 B:PHE189 4.7 12.7 1.0 CB B:TYR176 4.7 11.8 1.0 CE2 B:PHE178 4.8 9.9 1.0 O B:HOH499 4.8 10.2 1.0 CZ B:PHE189 4.8 15.3 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