Atomistry » Fluorine » PDB 3hky-3ig6 » 3ig6
Atomistry »
  Fluorine »
    PDB 3hky-3ig6 »
      3ig6 »

Fluorine in PDB 3ig6: Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex

Enzymatic activity of Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex

All present enzymatic activity of Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex:
3.4.21.73;

Protein crystallography data

The structure of Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex, PDB code: 3ig6 was solved by M.Adler, M.Whitlow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.83 / 1.83
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.855, 52.294, 72.580, 90.00, 90.23, 90.00
R / Rfree (%) 22.4 / 25.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex (pdb code 3ig6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex, PDB code: 3ig6:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3ig6

Go back to Fluorine Binding Sites List in 3ig6
Fluorine binding site 1 out of 4 in the Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F400

b:15.2
occ:1.00
 F22 B:438400 0.0 15.2 1.0
C18 B:438400 1.3 13.2 1.0
C17 B:438400 2.4 14.2 1.0
C19 B:438400 2.4 17.4 1.0
O15 B:438400 2.8 14.2 1.0
C41 B:438400 2.8 22.2 1.0
N23 B:438400 2.9 18.5 1.0
C11 B:438400 3.2 15.4 1.0
CD1 D:ILE60 3.2 14.4 1.0
CG1 D:ILE60 3.3 13.0 1.0
O D:HOH858 3.6 31.4 1.0
N16 B:438400 3.6 13.3 1.0
CD2 D:TYR94 3.7 12.2 1.0
C20 B:438400 3.7 14.9 1.0
C10 B:438400 3.7 12.2 1.0
C12 B:438400 3.8 16.4 1.0
CE2 D:TYR94 4.1 12.2 1.0
O D:TYR94 4.1 14.9 1.0
C21 B:438400 4.1 14.0 1.0
C38 B:438400 4.2 18.4 1.0
C40 B:438400 4.4 21.1 1.0
O B:HOH756 4.6 21.6 1.0
C9 B:438400 4.7 14.5 1.0
C13 B:438400 4.7 15.8 1.0
CB D:ILE60 4.7 10.0 1.0
O D:HOH611 4.8 20.2 1.0
CG D:TYR94 4.8 13.1 1.0
C39 B:438400 4.8 21.5 1.0
F24 B:438400 4.8 18.5 1.0
C D:TYR94 4.9 15.8 1.0

Fluorine binding site 2 out of 4 in 3ig6

Go back to Fluorine Binding Sites List in 3ig6
Fluorine binding site 2 out of 4 in the Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F400

b:18.5
occ:1.00
 F24 B:438400 0.0 18.5 1.0
C20 B:438400 1.3 14.9 1.0
C21 B:438400 2.4 14.0 1.0
C19 B:438400 2.4 17.4 1.0
O25 B:438400 2.7 16.1 1.0
C38 B:438400 2.8 18.4 1.0
O D:HOH851 2.8 28.2 1.0
N23 B:438400 2.8 18.5 1.0
O D:HOH695 3.1 24.5 1.0
NE2 B:HIS99 3.2 11.4 1.0
CE1 B:HIS99 3.3 12.1 1.0
CD2 B:HIS57 3.4 15.6 1.0
O B:HOH717 3.5 14.8 1.0
N16 B:438400 3.6 13.3 1.0
C18 B:438400 3.7 13.2 1.0
NE2 B:HIS57 3.7 13.4 1.0
C26 B:438400 4.1 15.0 1.0
C17 B:438400 4.2 14.2 1.0
CG B:HIS57 4.2 13.4 1.0
C39 B:438400 4.2 21.5 1.0
C41 B:438400 4.3 22.2 1.0
O D:TYR94 4.3 14.9 1.0
O35 B:438400 4.3 12.6 1.0
CD2 B:HIS99 4.6 12.9 1.0
ND1 B:HIS99 4.6 12.4 1.0
CE1 B:HIS57 4.6 12.9 1.0
C43 B:438400 4.6 25.7 1.0
C40 B:438400 4.6 21.1 1.0
O B:HOH843 4.7 36.2 1.0
C27 B:438400 4.8 17.7 1.0
F22 B:438400 4.8 15.2 1.0
ND1 B:HIS57 4.9 12.5 1.0
N42 B:438400 4.9 21.1 1.0
CB B:HIS57 4.9 13.7 1.0

Fluorine binding site 3 out of 4 in 3ig6

Go back to Fluorine Binding Sites List in 3ig6
Fluorine binding site 3 out of 4 in the Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:41.4
occ:1.00
 F22 D:438401 0.0 41.4 1.0
C18 D:438401 1.4 39.1 1.0
C17 D:438401 2.4 35.3 1.0
C19 D:438401 2.4 44.3 1.0
O15 D:438401 2.7 26.9 1.0
N23 D:438401 2.8 48.1 1.0
C38 D:438401 3.0 51.7 1.0
N16 D:438401 3.6 36.7 1.0
C20 D:438401 3.7 44.2 1.0
C11 D:438401 4.0 21.4 1.0
C41 D:438401 4.1 50.6 1.0
C21 D:438401 4.2 41.1 1.0
C39 D:438401 4.4 52.5 1.0
O B:HOH785 4.4 26.7 1.0
NE D:ARG217 4.4 41.7 1.0
C40 D:438401 4.5 52.1 1.0
N D:GLY218 4.5 22.0 1.0
O D:GLY216 4.5 16.2 1.0
CA D:ARG217 4.5 19.9 1.0
C12 D:438401 4.7 17.8 1.0
CG D:ARG217 4.7 27.6 1.0
O D:HOH852 4.7 47.4 1.0
CD2 B:TYR149 4.8 24.5 1.0
CD D:ARG217 4.8 36.0 1.0
F24 D:438401 4.8 47.6 1.0
O D:THR97A 4.9 19.7 1.0
C10 D:438401 5.0 18.6 1.0

Fluorine binding site 4 out of 4 in 3ig6

Go back to Fluorine Binding Sites List in 3ig6
Fluorine binding site 4 out of 4 in the Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Low Molecular Weigth Human Urokinase Type Plasminogen Activator 2-[6- (3'-Aminomethyl-Biphenyl-3-Yloxy)-4-(3-Dimethylamino-Pyrrolidin-1- Yl)-3,5-Difluoro-Pyridin-2-Yloxy]-4-Dimethylamino-Benzoic Acid Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:47.6
occ:1.00
 F24 D:438401 0.0 47.6 1.0
C20 D:438401 1.4 44.2 1.0
C21 D:438401 2.4 41.1 1.0
C19 D:438401 2.4 44.3 1.0
O25 D:438401 2.8 41.3 1.0
N23 D:438401 2.8 48.1 1.0
C41 D:438401 3.0 50.6 1.0
NH2 D:ARG217 3.0 45.5 1.0
O35 D:438401 3.6 48.2 1.0
N16 D:438401 3.6 36.7 1.0
C18 D:438401 3.7 39.1 1.0
CZ D:ARG217 3.8 44.0 1.0
C38 D:438401 4.1 51.7 1.0
C26 D:438401 4.1 42.1 1.0
C17 D:438401 4.2 35.3 1.0
NH1 D:ARG217 4.3 47.3 1.0
C40 D:438401 4.5 52.1 1.0
NE D:ARG217 4.6 41.7 1.0
C39 D:438401 4.6 52.5 1.0
CE2 B:TYR149 4.6 23.7 1.0
C33 D:438401 4.7 47.6 1.0
F22 D:438401 4.8 41.4 1.0
C32 D:438401 4.9 44.1 1.0

Reference:

C.W.West, M.Adler, D.Arnaiz, D.Chen, K.Chu, G.Gualtieri, E.Ho, C.Huwe, D.Light, G.Phillips, R.Pulk, D.Sukovich, M.Whitlow, S.Yuan, J.Bryant. Identification of Orally Bioavailable, Non-Amidine Inhibitors of Urokinase Plasminogen Activator (Upa) Bioorg.Med.Chem.Lett. V. 19 5712 2009.
ISSN: ISSN 0960-894X
PubMed: 19703768
DOI: 10.1016/J.BMCL.2009.08.008
Page generated: Mon Jul 14 17:00:27 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy