Zinc in PDB 8jud: Crystal Structure of Human Mmp-7 in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Human Mmp-7 in Complex with Inhibitor:
3.4.24.23;

The structure of Crystal Structure of Human Mmp-7 in Complex with Inhibitor, PDB code: 8jud was solved by M.Kamitani, K.Abe-Sato, Y.Oka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.69 / 1.50
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	77.35, 77.35, 62.37, 90, 90, 90
R / Rfree (%)	23.1 / 26

The structure of Crystal Structure of Human Mmp-7 in Complex with Inhibitor also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	2 atoms
Fluorine	(F)	3 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor (pdb code 8jud). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor, PDB code: 8jud:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor


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 Human Mmp-7 in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:16.4 occ:1.00 OD2 A:ASP165 2.0 17.0 1.0 NE2 A:HIS163 2.0 17.2 1.0 NE2 A:HIS178 2.1 15.1 1.0 ND1 A:HIS191 2.1 14.0 1.0 CD2 A:HIS163 2.9 18.7 1.0 CG A:ASP165 2.9 22.7 1.0 CE1 A:HIS178 3.0 15.8 1.0 CE1 A:HIS191 3.0 12.2 1.0 CD2 A:HIS178 3.1 15.7 1.0 CE1 A:HIS163 3.1 18.8 1.0 CG A:HIS191 3.1 13.7 1.0 OD1 A:ASP165 3.2 19.5 1.0 CB A:HIS191 3.5 13.8 1.0 CG A:HIS163 4.1 18.4 1.0 ND1 A:HIS178 4.1 13.9 1.0 NE2 A:HIS191 4.2 12.8 1.0 ND1 A:HIS163 4.2 16.8 1.0 CG A:HIS178 4.2 15.0 1.0 O A:TYR167 4.2 15.2 1.0 CD2 A:HIS191 4.2 14.0 1.0 CB A:ASP165 4.3 22.4 1.0 CE2 A:PHE180 4.3 17.2 1.0 CZ A:PHE169 4.8 15.2 1.0 CZ A:PHE180 4.8 16.4 1.0 CB A:TYR167 4.9 20.6 1.0 CA A:HIS191 4.9 14.1 1.0 CE2 A:PHE169 4.9 15.9 1.0 O A:HOH424 4.9 16.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor


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 Human Mmp-7 in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:15.9 occ:1.00 O B:GGL2 1.9 17.0 1.0 NE2 A:HIS218 2.1 13.5 1.0 NE2 A:HIS224 2.1 16.6 1.0 NE2 A:HIS214 2.1 17.4 1.0 C B:GGL2 2.8 17.9 1.0 OXT B:GGL2 3.0 20.6 1.0 CE1 A:HIS224 3.1 19.8 1.0 CE1 A:HIS218 3.1 15.8 1.0 CD2 A:HIS218 3.1 14.2 1.0 CD2 A:HIS214 3.1 13.5 1.0 CD2 A:HIS224 3.1 17.9 1.0 CE1 A:HIS214 3.1 14.9 1.0 ND1 A:HIS224 4.2 17.5 1.0 ND1 A:HIS218 4.2 14.3 1.0 ND1 A:HIS214 4.2 16.0 1.0 CA B:GGL2 4.2 18.5 1.0 CG A:HIS214 4.2 14.8 1.0 CG A:HIS224 4.2 17.0 1.0 CG A:HIS218 4.2 14.9 1.0 N B:GLY3 4.3 15.5 1.0 CD B:GGL2 4.4 14.8 1.0 C38 B:7SF1 4.5 21.0 1.0 C39 B:7SF1 4.6 19.6 1.0 CG B:GGL2 4.6 17.5 1.0 CE A:MET232 4.7 16.5 1.0 CA B:GLY3 4.8 15.0 1.0 NE2 A:GLN215 4.9 16.9 1.0 OE1 B:GGL2 4.9 15.1 1.0 CB B:GGL2 4.9 18.2 1.0

K.Abe-Sato, H.Tabuse, H.Kanazawa, M.Kamitani, M.Endo, S.Tokura, S.Wakabayashi, T.Yahara, T.Takeda, K.Hitaka, E.Gunji, N.Kojima, Y.Oka. Structure-Based Optimization and Biological Evaluation of Potent and Selective Mmp-7 Inhibitors For Kidney Fibrosis. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37861435
DOI: 10.1021/ACS.JMEDCHEM.3C01166