Fluorine 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
Zinc	(Zn)	2 atoms

The binding sites of Fluorine 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 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: 8jud:
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:21.9 occ:1.00 F47 B:7SF1 0.0 21.9 1.0 C44 B:7SF1 1.3 23.7 1.0 F46 B:7SF1 2.1 26.7 1.0 F45 B:7SF1 2.2 21.0 1.0 C42 B:7SF1 2.4 21.2 1.0 C40 B:7SF1 3.0 21.3 1.0 CL1 B:7SF1 3.1 26.1 1.0 C43 B:7SF1 3.5 20.9 1.0 CB A:ALA211 3.5 15.0 1.0 CD2 A:TYR236 3.6 28.6 1.0 CA A:ALA211 3.8 15.0 1.0 CG2 A:ILE206 4.2 17.6 1.0 CG A:TYR236 4.3 26.0 1.0 CE2 A:TYR236 4.3 25.0 1.0 CB A:TYR236 4.3 26.8 1.0 C39 B:7SF1 4.4 19.6 1.0 CD1 A:LEU176 4.4 18.1 1.0 N A:ALA211 4.6 16.6 1.0 C37 B:7SF1 4.7 19.1 1.0 C A:ALA211 4.9 14.1 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:26.7 occ:1.00 F46 B:7SF1 0.0 26.7 1.0 C44 B:7SF1 1.3 23.7 1.0 F47 B:7SF1 2.1 21.9 1.0 F45 B:7SF1 2.1 21.0 1.0 C42 B:7SF1 2.3 21.2 1.0 C43 B:7SF1 2.7 20.9 1.0 C40 B:7SF1 3.6 21.3 1.0 CB A:ALA177 3.7 15.2 1.0 NE2 A:GLN215 3.7 16.9 1.0 CB A:LEU176 3.8 17.6 1.0 CB A:ALA211 3.9 15.0 1.0 C37 B:7SF1 4.1 19.1 1.0 CD1 A:LEU176 4.3 18.1 1.0 CH2 A:TRP198 4.3 14.6 1.0 CL1 B:7SF1 4.5 26.1 1.0 CA A:ALA211 4.5 15.0 1.0 N A:ALA177 4.5 15.3 1.0 C A:LEU176 4.6 14.5 1.0 CZ3 A:TRP198 4.6 15.3 1.0 CA A:ALA177 4.7 14.9 1.0 CG A:LEU176 4.7 18.1 1.0 CD A:GLN215 4.7 15.2 1.0 C39 B:7SF1 4.7 19.6 1.0 O1 B:7SF1 4.8 17.7 1.0 CA A:LEU176 4.9 15.6 1.0 CG A:GLN215 4.9 13.6 1.0 O A:LEU176 4.9 15.3 1.0 O A:ALA211 4.9 13.3 1.0 C38 B:7SF1 4.9 21.0 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:21.0 occ:1.00 F45 B:7SF1 0.0 21.0 1.0 C44 B:7SF1 1.3 23.7 1.0 F46 B:7SF1 2.1 26.7 1.0 F47 B:7SF1 2.2 21.9 1.0 C42 B:7SF1 2.3 21.2 1.0 C40 B:7SF1 3.0 21.3 1.0 CL1 B:7SF1 3.2 26.1 1.0 NE2 A:GLN215 3.2 16.9 1.0 CA A:ALA211 3.3 15.0 1.0 C43 B:7SF1 3.4 20.9 1.0 O A:ALA211 3.4 13.3 1.0 CB A:ALA211 3.5 15.0 1.0 C A:ALA211 3.8 14.1 1.0 CB A:HIS214 3.9 14.0 1.0 CD2 A:HIS214 4.1 13.5 1.0 CG A:GLN215 4.1 13.6 1.0 CD A:GLN215 4.1 15.2 1.0 CG A:HIS214 4.1 14.8 1.0 C39 B:7SF1 4.3 19.6 1.0 N A:ALA211 4.5 16.6 1.0 C37 B:7SF1 4.6 19.1 1.0 N A:GLN215 4.8 13.1 1.0 CB A:ALA177 4.9 15.2 1.0 OXT B:GGL2 4.9 20.6 1.0 O A:TYR210 4.9 13.9 1.0 C38 B:7SF1 4.9 21.0 1.0 NE2 A:HIS214 5.0 17.4 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