Fluorine in PDB 8juf: 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: 8juf 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)	54.60 / 1.39
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	77.22, 77.22, 62.98, 90, 90, 90
R / Rfree (%)	19.7 / 22

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
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor (pdb code 8juf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor, PDB code: 8juf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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 B:F1 b:27.2 occ:1.00 F47 B:7SF1 0.0 27.2 1.0 C44 B:7SF1 1.3 30.6 1.0 F46 B:7SF1 2.1 31.7 1.0 F45 B:7SF1 2.1 29.8 1.0 C42 B:7SF1 2.2 25.9 1.0 C40 B:7SF1 2.9 24.3 1.0 CL1 B:7SF1 3.1 33.6 1.0 C43 B:7SF1 3.4 23.0 1.0 CD1 A:TYR236 3.5 31.2 1.0 CB A:ALA211 3.6 20.6 1.0 CA A:ALA211 3.9 19.5 1.0 CB A:TYR236 4.1 31.1 1.0 CG A:TYR236 4.1 33.7 1.0 CE1 A:TYR236 4.3 27.8 1.0 C39 B:7SF1 4.3 25.1 1.0 CD1 A:LEU176 4.4 28.1 1.0 CG2 A:ILE206 4.4 25.6 1.0 C37 B:7SF1 4.6 23.0 1.0 N A:ALA211 4.7 22.0 1.0 C38 B:7SF1 4.9 28.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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 B:F1 b:31.7 occ:1.00 F46 B:7SF1 0.0 31.7 1.0 C44 B:7SF1 1.3 30.6 1.0 F45 B:7SF1 2.1 29.8 1.0 F47 B:7SF1 2.1 27.2 1.0 C42 B:7SF1 2.3 25.9 1.0 C43 B:7SF1 2.7 23.0 1.0 CB A:ALA177 3.6 20.8 1.0 C40 B:7SF1 3.6 24.3 1.0 NE2 A:GLN215 3.7 22.7 1.0 CB A:ALA211 3.8 20.6 1.0 CB A:LEU176 3.9 22.8 1.0 C37 B:7SF1 4.1 23.0 1.0 CD1 A:LEU176 4.2 28.1 1.0 CH2 A:TRP198 4.3 25.0 1.0 CL1 B:7SF1 4.5 33.6 1.0 CA A:ALA211 4.5 19.5 1.0 N A:ALA177 4.5 22.3 1.0 CZ3 A:TRP198 4.6 20.1 1.0 CA A:ALA177 4.7 20.5 1.0 CG A:LEU176 4.7 28.0 1.0 O1 B:7SF1 4.7 26.1 1.0 C A:LEU176 4.7 16.6 1.0 CD A:GLN215 4.7 20.3 1.0 C39 B:7SF1 4.8 25.1 1.0 CG A:GLN215 4.9 20.0 1.0 O A:ALA211 4.9 20.6 1.0 C38 B:7SF1 5.0 28.1 1.0 O A:LEU176 5.0 19.4 1.0 CA A:LEU176 5.0 23.4 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Mmp-7 in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F1 b:29.8 occ:1.00 F45 B:7SF1 0.0 29.8 1.0 C44 B:7SF1 1.3 30.6 1.0 F46 B:7SF1 2.1 31.7 1.0 F47 B:7SF1 2.1 27.2 1.0 C42 B:7SF1 2.2 25.9 1.0 C40 B:7SF1 2.9 24.3 1.0 NE2 A:GLN215 3.1 22.7 1.0 CL1 B:7SF1 3.2 33.6 1.0 C43 B:7SF1 3.3 23.0 1.0 O A:ALA211 3.4 20.6 1.0 CA A:ALA211 3.4 19.5 1.0 CB A:ALA211 3.5 20.6 1.0 C A:ALA211 3.9 17.4 1.0 CB A:HIS214 3.9 19.1 1.0 CD A:GLN215 4.1 20.3 1.0 CD2 A:HIS214 4.1 17.9 1.0 CG A:GLN215 4.1 20.0 1.0 CG A:HIS214 4.2 19.5 1.0 C39 B:7SF1 4.2 25.1 1.0 C37 B:7SF1 4.5 23.0 1.0 N A:ALA211 4.6 22.0 1.0 CB A:ALA177 4.7 20.8 1.0 N A:GLN215 4.8 18.6 1.0 C38 B:7SF1 4.9 28.1 1.0 O B:GGL2 4.9 28.3 1.0 O A:TYR210 5.0 21.0 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