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Fluorine in PDB 5tqg: Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione

Enzymatic activity of Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione

All present enzymatic activity of Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione:
3.4.21.21;

Protein crystallography data

The structure of Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione, PDB code: 5tqg was solved by A.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.58 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.800, 95.800, 117.100, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.4

Other elements in 5tqg:

The structure of Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione (pdb code 5tqg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione, PDB code: 5tqg:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5tqg

Go back to Fluorine Binding Sites List in 5tqg
Fluorine binding site 1 out of 3 in the Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F301

b:35.8
occ:1.00
 F43 H:7KS301 0.0 35.8 1.0
C38 H:7KS301 1.4 31.0 1.0
C33 H:7KS301 2.4 25.4 1.0
C37 H:7KS301 2.4 27.2 1.0
H73 H:7KS301 2.5 22.3 0.0
H74 H:7KS301 2.7 27.2 0.0
C34 H:7KS301 2.9 22.3 1.0
N H:GLY219 3.0 36.9 1.0
C H:GLY219 3.2 36.6 1.0
O H:HOH577 3.3 35.1 1.0
CA H:GLY219 3.3 35.2 1.0
O H:GLY216 3.4 28.7 1.0
C H:GLY216 3.5 32.4 1.0
N H:CYS220 3.5 28.1 1.0
O H:HOH688 3.5 18.4 1.0
O H:HOH572 3.5 26.8 1.0
O H:GLY219 3.6 37.5 1.0
N36 H:7KS301 3.6 28.4 1.0
C32 H:7KS301 3.7 25.7 1.0
H52 H:7KS301 3.8 23.2 0.0
N H:GLN217 3.9 34.0 1.0
CA H:GLY216 3.9 26.5 1.0
C H:GLN217 4.0 41.7 1.0
CA H:CYS220 4.1 27.8 0.5
C35 H:7KS301 4.1 27.1 1.0
N H:GLY216 4.2 25.6 1.0
CA H:CYS220 4.2 25.1 0.5
C29 H:7KS301 4.2 23.2 1.0
CA H:GLN217 4.3 35.5 1.0
H49 H:7KS301 4.5 21.1 0.0
CB H:CYS220 4.5 28.1 0.5
C7 H:7KS301 4.5 23.1 1.0
O H:HOH529 4.8 34.7 1.0
CB H:CYS220 4.8 22.9 0.5
C31 H:7KS301 4.9 25.8 1.0
O H:GLN217 4.9 43.9 1.0
H51 H:7KS301 5.0 23.3 0.0

Fluorine binding site 2 out of 3 in 5tqg

Go back to Fluorine Binding Sites List in 5tqg
Fluorine binding site 2 out of 3 in the Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F301

b:39.9
occ:1.00
 F46 H:7KS301 0.0 39.9 1.0
C45 H:7KS301 1.4 37.7 1.0
H79 H:7KS301 2.0 37.8 0.0
F47 H:7KS301 2.1 41.4 1.0
C44 H:7KS301 2.4 30.2 1.0
H78 H:7KS301 2.7 30.3 0.0
O42 H:7KS301 2.7 25.9 1.0
H77 H:7KS301 3.3 30.3 0.0
H69 H:7KS301 3.4 21.1 0.0
CG H:PRO170I 3.7 67.9 1.0
CG2 H:THR99 3.8 25.9 1.0
C5 H:7KS301 4.0 24.6 1.0
H67 H:7KS301 4.2 21.5 0.0
O H:HOH613 4.3 35.3 1.0
O H:HOH453 4.3 36.2 1.0
CD H:PRO170I 4.3 63.7 1.0
C27 H:7KS301 4.4 21.0 1.0
C24 H:7KS301 4.7 21.4 1.0
H51 H:7KS301 4.7 23.3 0.0
H68 H:7KS301 4.8 21.1 0.0
C6 H:7KS301 4.9 23.2 1.0
C4 H:7KS301 4.9 22.6 1.0

Fluorine binding site 3 out of 3 in 5tqg

Go back to Fluorine Binding Sites List in 5tqg
Fluorine binding site 3 out of 3 in the Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Factor Viia in Complex with the Inhibitor (5R,11R)-11-[(1-Amino-4- Fluoroisoquinolin-6-Yl)Amino]-16-(Cyclopropylsulfonyl)-7-(2,2- Difluoroethoxy)-5,13-Dimethyl-2,13-Diazatricyclo[13.3.1.1~6, 10~]Icosa-1(19),6(20),7,9,15,17-Hexaene-3,12-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F301

b:41.4
occ:1.00
 F47 H:7KS301 0.0 41.4 1.0
C45 H:7KS301 1.4 37.7 1.0
H79 H:7KS301 2.0 37.8 0.0
F46 H:7KS301 2.1 39.9 1.0
C44 H:7KS301 2.3 30.2 1.0
H78 H:7KS301 2.5 30.3 0.0
H77 H:7KS301 2.7 30.3 0.0
NE2 H:GLN217 3.1 85.1 1.0
CD H:PRO170I 3.1 63.7 1.0
CG H:PRO170I 3.3 67.9 1.0
O42 H:7KS301 3.5 25.9 1.0
CD H:GLN217 4.1 92.9 1.0
CZ3 H:TRP215 4.2 23.8 1.0
CE3 H:TRP215 4.3 22.3 1.0
OE1 H:GLN217 4.5 92.1 1.0
N H:PRO170I 4.5 62.7 1.0
H51 H:7KS301 4.5 23.3 0.0
C5 H:7KS301 4.7 24.6 1.0
CB H:PRO170I 4.8 63.2 1.0
O H:HOH645 4.8 65.4 1.0
CG2 H:THR99 4.9 25.9 1.0

Reference:

J.M.Richter, D.L.Cheney, J.A.Bates, A.Wei, J.M.Luettgen, A.R.Rendina, T.M.Harper, R.Narayanan, P.C.Wong, D.Seiffert, R.R.Wexler, E.S.Priestley. Design and Synthesis of Novel Meta-Linked Phenylglycine Macrocyclic Fviia Inhibitors. Acs Med Chem Lett V. 8 67 2017.
ISSN: ISSN 1948-5875
PubMed: 28105277
DOI: 10.1021/ACSMEDCHEMLETT.6B00375
Page generated: Thu Aug 1 15:20:36 2024

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