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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy