Fluorine in PDB 8k4z: 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: 8k4z was solved by M.Kamitani, M.Mima, Y.Oka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.60 / 1.70
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	75.799, 75.799, 60.53, 90, 90, 90
R / Rfree (%)	20.3 / 23.9

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

Chlorine	(Cl)	2 atoms
Iodine	(I)	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 8k4z). 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: 8k4z:
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:15.4 occ:1.00 F47 B:7SF1 0.0 15.4 1.0 C44 B:7SF1 1.3 15.0 1.0 F45 B:7SF1 2.1 16.1 1.0 F46 B:7SF1 2.1 16.9 1.0 C42 B:7SF1 2.3 14.2 1.0 C40 B:7SF1 2.9 14.8 1.0 CL1 B:7SF1 3.0 18.2 1.0 C43 B:7SF1 3.4 13.0 1.0 CB A:ALA211 3.6 10.0 1.0 CD1 A:TYR236 3.6 17.0 1.0 CA A:ALA211 3.8 10.6 1.0 CG2 A:ILE206 4.1 13.0 1.0 C39 B:7SF1 4.3 14.4 1.0 CB A:TYR236 4.3 18.7 1.0 CG A:TYR236 4.3 17.6 1.0 CE1 A:TYR236 4.3 15.9 1.0 CD1 A:LEU176 4.5 12.8 1.0 C37 B:7SF1 4.6 13.1 1.0 N A:ALA211 4.6 10.7 1.0 C A:ALA211 4.9 10.2 1.0 O A:ALA211 4.9 9.6 1.0 C38 B:7SF1 5.0 13.6 1.0 CA A:TYR236 5.0 21.2 1.0 NE2 A:GLN215 5.0 12.0 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:16.9 occ:1.00 F46 B:7SF1 0.0 16.9 1.0 C44 B:7SF1 1.3 15.0 1.0 F47 B:7SF1 2.1 15.4 1.0 F45 B:7SF1 2.1 16.1 1.0 C42 B:7SF1 2.3 14.2 1.0 C40 B:7SF1 2.9 14.8 1.0 CL1 B:7SF1 3.1 18.2 1.0 NE2 A:GLN215 3.1 12.0 1.0 CA A:ALA211 3.3 10.6 1.0 O A:ALA211 3.3 9.6 1.0 C43 B:7SF1 3.3 13.0 1.0 CB A:ALA211 3.5 10.0 1.0 C A:ALA211 3.7 10.2 1.0 CB A:HIS214 3.9 9.7 1.0 CD2 A:HIS214 4.0 10.1 1.0 CD A:GLN215 4.0 11.2 1.0 CG A:GLN215 4.1 10.8 1.0 CG A:HIS214 4.1 9.8 1.0 C39 B:7SF1 4.2 14.4 1.0 C37 B:7SF1 4.5 13.1 1.0 N A:ALA211 4.5 10.7 1.0 CB A:ALA177 4.6 8.9 1.0 N A:GLN215 4.7 10.5 1.0 C38 B:7SF1 4.9 13.6 1.0 O A:TYR210 4.9 10.9 1.0 NE2 A:HIS214 5.0 10.0 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:16.1 occ:1.00 F45 B:7SF1 0.0 16.1 1.0 C44 B:7SF1 1.3 15.0 1.0 F47 B:7SF1 2.1 15.4 1.0 F46 B:7SF1 2.1 16.9 1.0 C42 B:7SF1 2.3 14.2 1.0 C43 B:7SF1 2.7 13.0 1.0 CB A:ALA177 3.5 8.9 1.0 C40 B:7SF1 3.6 14.8 1.0 CB A:LEU176 3.7 11.2 1.0 NE2 A:GLN215 3.8 12.0 1.0 CB A:ALA211 3.9 10.0 1.0 C37 B:7SF1 4.1 13.1 1.0 CH2 A:TRP198 4.1 11.3 1.0 CD1 A:LEU176 4.3 12.8 1.0 CZ3 A:TRP198 4.4 10.9 1.0 N A:ALA177 4.4 9.0 1.0 CL1 B:7SF1 4.4 18.2 1.0 CA A:ALA211 4.4 10.6 1.0 C A:LEU176 4.5 9.7 1.0 CA A:ALA177 4.5 8.9 1.0 CG A:LEU176 4.6 11.9 1.0 O A:LEU176 4.7 9.8 1.0 CA A:LEU176 4.7 10.7 1.0 C39 B:7SF1 4.7 14.4 1.0 O35 B:7SF1 4.7 13.3 1.0 CD A:GLN215 4.8 11.2 1.0 CG A:GLN215 4.9 10.8 1.0 CG2 A:ILE206 4.9 13.0 1.0 O A:ALA211 4.9 9.6 1.0 C38 B:7SF1 4.9 13.6 1.0

Y.Oka, K.Abe-Sato, H.Tabuse, Y.Yasukawa, T.Yahara, T.Nishimoto, M.Kamitani, T.Fukunaga, N.Ochiai, T.Kumasaka-Abe, K.Hitaka, E.Gunji, H.Ohara, T.Takeda, N.Kojima, T.Asami. Discovery of TP0628103: A Selective Mmp-7 Inhibitor Based on the Mitigation of Oatp Substrate Recognition Through Isoelectric Point Shift Strategy To Be Published.