Fluorine in PDB 8jug: Crystal Structure of Human Mmp-7 in Complex with Inhibitor

Enzymatic activity of 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;

Protein crystallography data

The structure of Crystal Structure of Human Mmp-7 in Complex with Inhibitor, PDB code: 8jug 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) 48.05 / 1.30
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 76.06, 76.06, 61.89, 90, 90, 90
R / Rfree (%) 22.1 / 23.8

Other elements in 8jug:

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

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor (pdb code 8jug). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Mmp-7 in Complex with Inhibitor, PDB code: 8jug:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8jug

Go back to Fluorine Binding Sites List in 8jug
Fluorine binding site 1 out of 6 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
C:F1

b:16.8
occ:0.50
 F47 C:7SF1 0.0 16.8 0.5
F47 C:7SF1 0.0 13.6 0.5
C44 C:7SF1 1.3 16.7 0.5
C44 C:7SF1 1.3 13.6 0.5
F46 C:7SF1 2.1 17.3 0.5
F45 C:7SF1 2.1 17.5 0.5
F46 C:7SF1 2.1 13.7 0.5
F45 C:7SF1 2.1 13.9 0.5
C42 C:7SF1 2.3 15.5 0.5
C42 C:7SF1 2.4 12.9 0.5
C43 C:7SF1 2.7 13.8 0.5
C43 C:7SF1 2.7 12.0 0.5
CB A:ALA177 3.6 9.7 1.0
C40 C:7SF1 3.6 15.3 0.5
C40 C:7SF1 3.6 12.7 0.5
CB A:ALA211 3.7 9.7 1.0
CB A:LEU176 3.7 11.6 1.0
NE2 A:GLN215 3.8 10.0 1.0
C37 C:7SF1 4.1 12.8 0.5
C37 C:7SF1 4.1 11.7 0.5
CD1 A:LEU176 4.1 13.1 1.0
CH2 A:TRP198 4.2 11.7 1.0
CL1 C:7SF1 4.4 18.8 0.5
CL1 C:7SF1 4.4 14.7 0.5
CA A:ALA211 4.4 9.4 1.0
CZ3 A:TRP198 4.4 10.8 1.0
N A:ALA177 4.5 10.6 1.0
CG A:LEU176 4.6 12.7 1.0
C A:LEU176 4.6 9.7 1.0
CA A:ALA177 4.7 10.4 1.0
O35 C:7SF1 4.7 10.5 0.5
O35 C:7SF1 4.7 10.4 0.5
CD A:GLN215 4.7 8.0 1.0
C39 C:7SF1 4.8 14.9 0.5
C39 C:7SF1 4.8 12.7 0.5
CA A:LEU176 4.8 10.5 1.0
CG A:GLN215 4.8 9.1 1.0
O A:ALA211 4.9 9.4 1.0
O A:LEU176 4.9 10.5 1.0
C38 C:7SF1 4.9 14.4 0.5
C38 C:7SF1 4.9 12.7 0.5

Fluorine binding site 2 out of 6 in 8jug

Go back to Fluorine Binding Sites List in 8jug
Fluorine binding site 2 out of 6 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
C:F1

b:13.6
occ:0.50
 F47 C:7SF1 0.0 13.6 0.5
F47 C:7SF1 0.0 16.8 0.5
C44 C:7SF1 1.3 16.7 0.5
C44 C:7SF1 1.3 13.6 0.5
F46 C:7SF1 2.1 17.3 0.5
F46 C:7SF1 2.1 13.7 0.5
F45 C:7SF1 2.1 17.5 0.5
F45 C:7SF1 2.1 13.9 0.5
C42 C:7SF1 2.3 15.5 0.5
C42 C:7SF1 2.4 12.9 0.5
C43 C:7SF1 2.7 13.8 0.5
C43 C:7SF1 2.7 12.0 0.5
CB A:ALA177 3.6 9.7 1.0
C40 C:7SF1 3.6 15.3 0.5
CB A:ALA211 3.6 9.7 1.0
C40 C:7SF1 3.6 12.7 0.5
CB A:LEU176 3.8 11.6 1.0
NE2 A:GLN215 3.8 10.0 1.0
C37 C:7SF1 4.1 12.8 0.5
C37 C:7SF1 4.1 11.7 0.5
CD1 A:LEU176 4.2 13.1 1.0
CH2 A:TRP198 4.2 11.7 1.0
CL1 C:7SF1 4.3 18.8 0.5
CA A:ALA211 4.4 9.4 1.0
CL1 C:7SF1 4.4 14.7 0.5
CZ3 A:TRP198 4.4 10.8 1.0
N A:ALA177 4.5 10.6 1.0
CG A:LEU176 4.6 12.7 1.0
C A:LEU176 4.6 9.7 1.0
CA A:ALA177 4.7 10.4 1.0
CD A:GLN215 4.7 8.0 1.0
O35 C:7SF1 4.7 10.5 0.5
O35 C:7SF1 4.7 10.4 0.5
C39 C:7SF1 4.7 14.9 0.5
C39 C:7SF1 4.8 12.7 0.5
CG A:GLN215 4.8 9.1 1.0
CA A:LEU176 4.8 10.5 1.0
O A:ALA211 4.9 9.4 1.0
C38 C:7SF1 4.9 14.4 0.5
C38 C:7SF1 4.9 12.7 0.5
O A:LEU176 4.9 10.5 1.0

Fluorine binding site 3 out of 6 in 8jug

Go back to Fluorine Binding Sites List in 8jug
Fluorine binding site 3 out of 6 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
C:F1

b:17.3
occ:0.50
 F46 C:7SF1 0.0 17.3 0.5
F46 C:7SF1 0.1 13.7 0.5
C44 C:7SF1 1.3 13.6 0.5
C44 C:7SF1 1.3 16.7 0.5
F47 C:7SF1 2.1 13.6 0.5
F47 C:7SF1 2.1 16.8 0.5
F45 C:7SF1 2.1 13.9 0.5
F45 C:7SF1 2.2 17.5 0.5
C42 C:7SF1 2.3 15.5 0.5
C42 C:7SF1 2.3 12.9 0.5
C40 C:7SF1 3.0 15.3 0.5
C40 C:7SF1 3.0 12.7 0.5
CL1 C:7SF1 3.1 18.8 0.5
CL1 C:7SF1 3.1 14.7 0.5
NE2 A:GLN215 3.2 10.0 1.0
CA A:ALA211 3.3 9.4 1.0
CB A:ALA211 3.3 9.7 1.0
C43 C:7SF1 3.3 12.0 0.5
C43 C:7SF1 3.3 13.8 0.5
O A:ALA211 3.3 9.4 1.0
C A:ALA211 3.7 8.8 1.0
CB A:HIS214 3.8 9.1 1.0
CG A:GLN215 4.0 9.1 1.0
CG A:HIS214 4.1 9.2 1.0
CD A:GLN215 4.1 8.0 1.0
CD2 A:HIS214 4.1 9.1 1.0
C39 C:7SF1 4.3 14.9 0.5
C39 C:7SF1 4.3 12.7 0.5
C37 C:7SF1 4.5 12.8 0.5
C37 C:7SF1 4.5 11.7 0.5
N A:ALA211 4.5 10.6 1.0
CB A:ALA177 4.7 9.7 1.0
N A:GLN215 4.7 8.7 1.0
OXT C:GGL2 4.8 11.5 0.5
OXT C:GGL2 4.8 13.1 0.5
C38 C:7SF1 4.9 14.4 0.5
O A:TYR210 4.9 10.6 1.0
C38 C:7SF1 4.9 12.7 0.5

Fluorine binding site 4 out of 6 in 8jug

Go back to Fluorine Binding Sites List in 8jug
Fluorine binding site 4 out of 6 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 4 of Crystal Structure of Human Mmp-7 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1

b:13.7
occ:0.50
 F46 C:7SF1 0.0 13.7 0.5
F46 C:7SF1 0.1 17.3 0.5
C44 C:7SF1 1.3 13.6 0.5
C44 C:7SF1 1.3 16.7 0.5
F47 C:7SF1 2.1 13.6 0.5
F47 C:7SF1 2.1 16.8 0.5
F45 C:7SF1 2.1 13.9 0.5
F45 C:7SF1 2.2 17.5 0.5
C42 C:7SF1 2.3 15.5 0.5
C42 C:7SF1 2.3 12.9 0.5
C40 C:7SF1 2.9 15.3 0.5
C40 C:7SF1 3.0 12.7 0.5
CL1 C:7SF1 3.1 18.8 0.5
CL1 C:7SF1 3.1 14.7 0.5
NE2 A:GLN215 3.2 10.0 1.0
CA A:ALA211 3.3 9.4 1.0
C43 C:7SF1 3.3 12.0 0.5
C43 C:7SF1 3.3 13.8 0.5
O A:ALA211 3.3 9.4 1.0
CB A:ALA211 3.3 9.7 1.0
C A:ALA211 3.8 8.8 1.0
CB A:HIS214 3.8 9.1 1.0
CG A:HIS214 4.0 9.2 1.0
CG A:GLN215 4.0 9.1 1.0
CD2 A:HIS214 4.0 9.1 1.0
CD A:GLN215 4.0 8.0 1.0
C39 C:7SF1 4.2 14.9 0.5
C39 C:7SF1 4.3 12.7 0.5
C37 C:7SF1 4.5 12.8 0.5
C37 C:7SF1 4.5 11.7 0.5
N A:ALA211 4.6 10.6 1.0
N A:GLN215 4.7 8.7 1.0
CB A:ALA177 4.7 9.7 1.0
OXT C:GGL2 4.8 11.5 0.5
OXT C:GGL2 4.8 13.1 0.5
C38 C:7SF1 4.9 14.4 0.5
C38 C:7SF1 4.9 12.7 0.5
O A:TYR210 4.9 10.6 1.0
CA A:HIS214 5.0 9.2 1.0

Fluorine binding site 5 out of 6 in 8jug

Go back to Fluorine Binding Sites List in 8jug
Fluorine binding site 5 out of 6 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 5 of Crystal Structure of Human Mmp-7 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1

b:17.5
occ:0.50
 F45 C:7SF1 0.0 17.5 0.5
F45 C:7SF1 0.1 13.9 0.5
C44 C:7SF1 1.3 16.7 0.5
C44 C:7SF1 1.3 13.6 0.5
F47 C:7SF1 2.1 13.6 0.5
F47 C:7SF1 2.1 16.8 0.5
F46 C:7SF1 2.2 17.3 0.5
F46 C:7SF1 2.2 13.7 0.5
C42 C:7SF1 2.3 15.5 0.5
C42 C:7SF1 2.3 12.9 0.5
C40 C:7SF1 2.9 15.3 0.5
CL1 C:7SF1 2.9 18.8 0.5
C40 C:7SF1 3.0 12.7 0.5
CL1 C:7SF1 3.0 14.7 0.5
CD1 A:TYR236 3.3 16.4 1.0
CB A:ALA211 3.4 9.7 1.0
C43 C:7SF1 3.4 13.8 0.5
C43 C:7SF1 3.4 12.0 0.5
CA A:ALA211 3.8 9.4 1.0
CE1 A:TYR236 4.0 17.1 1.0
CG A:TYR236 4.1 17.1 1.0
CB A:TYR236 4.2 18.6 1.0
C39 C:7SF1 4.2 14.9 0.5
C39 C:7SF1 4.2 12.7 0.5
CD1 A:LEU176 4.3 13.1 1.0
CG2 A:ILE206 4.4 9.9 1.0
C37 C:7SF1 4.6 12.8 0.5
C37 C:7SF1 4.6 11.7 0.5
N A:ALA211 4.7 10.6 1.0
C38 C:7SF1 4.9 14.4 0.5
C38 C:7SF1 4.9 12.7 0.5
C A:ALA211 4.9 8.8 1.0
O A:ALA211 5.0 9.4 1.0

Fluorine binding site 6 out of 6 in 8jug

Go back to Fluorine Binding Sites List in 8jug
Fluorine binding site 6 out of 6 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 6 of Crystal Structure of Human Mmp-7 in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1

b:13.9
occ:0.50
 F45 C:7SF1 0.0 13.9 0.5
F45 C:7SF1 0.1 17.5 0.5
C44 C:7SF1 1.3 16.7 0.5
C44 C:7SF1 1.3 13.6 0.5
F47 C:7SF1 2.1 13.6 0.5
F46 C:7SF1 2.1 17.3 0.5
F47 C:7SF1 2.1 16.8 0.5
F46 C:7SF1 2.1 13.7 0.5
C42 C:7SF1 2.3 15.5 0.5
C42 C:7SF1 2.3 12.9 0.5
CL1 C:7SF1 2.9 18.8 0.5
C40 C:7SF1 2.9 15.3 0.5
C40 C:7SF1 2.9 12.7 0.5
CL1 C:7SF1 2.9 14.7 0.5
CD1 A:TYR236 3.3 16.4 1.0
CB A:ALA211 3.4 9.7 1.0
C43 C:7SF1 3.4 13.8 0.5
C43 C:7SF1 3.4 12.0 0.5
CA A:ALA211 3.8 9.4 1.0
CE1 A:TYR236 4.0 17.1 1.0
CG A:TYR236 4.1 17.1 1.0
C39 C:7SF1 4.2 14.9 0.5
CB A:TYR236 4.2 18.6 1.0
C39 C:7SF1 4.2 12.7 0.5
CD1 A:LEU176 4.4 13.1 1.0
CG2 A:ILE206 4.4 9.9 1.0
C37 C:7SF1 4.6 12.8 0.5
C37 C:7SF1 4.6 11.7 0.5
N A:ALA211 4.7 10.6 1.0
C38 C:7SF1 4.9 14.4 0.5
C38 C:7SF1 4.9 12.7 0.5
C A:ALA211 4.9 8.8 1.0
O A:ALA211 5.0 9.4 1.0
CD2 A:TYR210 5.0 13.8 1.0

Reference:

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
Page generated: Fri Aug 2 21:02:43 2024

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