Fluorine in PDB 7wxx: 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: 7wxx was solved by M.Kamitani, Y.Oka, H.Tabuse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.70 / 1.50
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	77.36, 77.36, 62.71, 90, 90, 90
R / Rfree (%)	17 / 20.3

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

Calcium	(Ca)	2 atoms
Zinc	(Zn)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor (pdb code 7wxx). 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: 7wxx:
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:27.6 occ:1.00 F47 B:7SF1 0.0 27.6 1.0 C44 B:7SF1 1.3 31.0 1.0 F46 B:7SF1 2.1 33.9 1.0 F45 B:7SF1 2.2 27.4 1.0 C42 B:7SF1 2.4 24.5 1.0 CL1 B:7SF1 3.1 31.3 1.0 C40 B:7SF1 3.1 25.2 1.0 CB A:ALA211 3.5 18.5 1.0 C43 B:7SF1 3.5 22.5 1.0 CD2 A:TYR236 3.6 27.9 1.0 CA A:ALA211 3.8 16.6 1.0 CG2 A:ILE206 4.2 21.0 1.0 CG A:TYR236 4.3 31.3 1.0 CB A:TYR236 4.3 33.2 1.0 CE2 A:TYR236 4.3 25.6 1.0 C39 B:7SF1 4.4 23.4 1.0 CD1 A:LEU176 4.5 24.4 1.0 N A:ALA211 4.6 18.4 1.0 C37 B:7SF1 4.7 21.7 1.0 C A:ALA211 4.9 15.9 1.0 O A:ALA211 5.0 18.4 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:33.9 occ:1.00 F46 B:7SF1 0.0 33.9 1.0 C44 B:7SF1 1.3 31.0 1.0 F47 B:7SF1 2.1 27.6 1.0 F45 B:7SF1 2.1 27.4 1.0 C42 B:7SF1 2.4 24.5 1.0 C43 B:7SF1 2.7 22.5 1.0 C40 B:7SF1 3.7 25.2 1.0 CB A:ALA177 3.7 16.7 1.0 CB A:ALA211 3.8 18.5 1.0 NE2 A:GLN215 3.8 20.6 1.0 CB A:LEU176 3.9 19.2 1.0 C37 B:7SF1 4.1 21.7 1.0 CD1 A:LEU176 4.2 24.4 1.0 CH2 A:TRP198 4.3 18.7 1.0 CA A:ALA211 4.5 16.6 1.0 CL1 B:7SF1 4.5 31.3 1.0 N A:ALA177 4.5 15.8 1.0 CZ3 A:TRP198 4.6 17.2 1.0 C A:LEU176 4.7 14.8 1.0 CA A:ALA177 4.7 16.2 1.0 CG A:LEU176 4.7 22.4 1.0 O36 B:7SF1 4.7 24.8 1.0 CD A:GLN215 4.8 18.4 1.0 C39 B:7SF1 4.8 23.4 1.0 O A:ALA211 4.9 18.4 1.0 CG A:GLN215 4.9 17.9 1.0 CA A:LEU176 5.0 18.1 1.0 O A:LEU176 5.0 17.6 1.0 C38 B:7SF1 5.0 26.6 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:27.4 occ:1.00 F45 B:7SF1 0.0 27.4 1.0 C44 B:7SF1 1.3 31.0 1.0 F46 B:7SF1 2.1 33.9 1.0 F47 B:7SF1 2.2 27.6 1.0 C42 B:7SF1 2.3 24.5 1.0 C40 B:7SF1 3.0 25.2 1.0 CL1 B:7SF1 3.1 31.3 1.0 NE2 A:GLN215 3.2 20.6 1.0 C43 B:7SF1 3.3 22.5 1.0 CA A:ALA211 3.3 16.6 1.0 O A:ALA211 3.4 18.4 1.0 CB A:ALA211 3.4 18.5 1.0 C A:ALA211 3.8 15.9 1.0 CB A:HIS214 3.9 16.5 1.0 CD2 A:HIS214 4.0 16.6 1.0 CG A:HIS214 4.1 18.4 1.0 CD A:GLN215 4.1 18.4 1.0 CG A:GLN215 4.2 17.9 1.0 C39 B:7SF1 4.3 23.4 1.0 N A:ALA211 4.5 18.4 1.0 C37 B:7SF1 4.5 21.7 1.0 N A:GLN215 4.8 16.0 1.0 CB A:ALA177 4.9 16.7 1.0 O A:TYR210 4.9 17.8 1.0 C38 B:7SF1 4.9 26.6 1.0 NE2 A:HIS214 5.0 18.7 1.0

H.Tabuse, K.Abe-Sato, H.Kanazawa, M.Yashiro, Y.Tamura, M.Kamitani, K.Hitaka, E.Gunji, A.Mitani, N.Kojima, Y.Oka. Discovery of Highly Potent and Selective Matrix Metalloproteinase-7 Inhibitors By Hybridizing the S1' Subsite Binder with Short Peptides. J.Med.Chem. V. 65 13253 2022.
ISSN: ISSN 0022-2623
PubMed: 36137271
DOI: 10.1021/ACS.JMEDCHEM.2C01088