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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: Wed Jul 31 19:29:12 2024

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