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Fluorine in PDB 3cs7: Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One

Enzymatic activity of Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One

All present enzymatic activity of Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One, PDB code: 3cs7 was solved by R.S.Alexander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.500, 72.600, 79.000, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 27.4

Other elements in 3cs7:

The structure of Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One (pdb code 3cs7). 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 Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One, PDB code: 3cs7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3cs7

Go back to Fluorine Binding Sites List in 3cs7
Fluorine binding site 1 out of 3 in the Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F298

b:43.7
occ:1.00
 F1 A:LG0298 0.0 43.7 1.0
C11 A:LG0298 1.3 42.8 1.0
F2 A:LG0298 2.2 42.2 1.0
F3 A:LG0298 2.2 43.4 1.0
C10 A:LG0298 2.4 41.1 1.0
N6 A:LG0298 2.8 38.8 1.0
NH1 A:ARG143 3.2 39.1 1.0
CB A:GLN192 3.5 31.1 1.0
O A:GLU146 3.5 38.1 1.0
C12 A:LG0298 3.7 40.0 1.0
SG A:CYS220 3.8 33.2 1.0
CZ A:ARG143 3.9 37.6 1.0
SG A:CYS191 4.0 34.9 1.0
CD A:ARG143 4.0 35.2 1.0
CG A:GLU146 4.0 42.2 1.0
N1 A:LG0298 4.2 37.7 1.0
NE A:ARG143 4.2 37.6 1.0
N A:GLN192 4.3 27.9 1.0
CG A:GLN192 4.4 35.3 1.0
OE1 A:GLN192 4.4 41.2 1.0
C A:GLU146 4.4 38.3 1.0
CA A:GLN192 4.5 27.6 1.0
CA A:GLU146 4.5 38.3 1.0
C19 A:LG0298 4.6 41.1 1.0
C13 A:LG0298 4.6 40.0 1.0
NH2 A:ARG143 4.7 38.7 1.0
CD A:GLN192 4.9 38.9 1.0
CB A:GLU146 4.9 38.2 1.0

Fluorine binding site 2 out of 3 in 3cs7

Go back to Fluorine Binding Sites List in 3cs7
Fluorine binding site 2 out of 3 in the Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F298

b:42.2
occ:1.00
 F2 A:LG0298 0.0 42.2 1.0
C11 A:LG0298 1.3 42.8 1.0
F1 A:LG0298 2.2 43.7 1.0
F3 A:LG0298 2.2 43.4 1.0
C10 A:LG0298 2.3 41.1 1.0
C12 A:LG0298 2.9 40.0 1.0
C19 A:LG0298 3.1 41.1 1.0
N6 A:LG0298 3.5 38.8 1.0
OE1 A:GLN192 3.6 41.2 1.0
NH1 A:ARG143 3.9 39.1 1.0
C13 A:LG0298 4.2 40.0 1.0
CB A:GLN192 4.3 31.1 1.0
CZ A:ARG143 4.4 37.6 1.0
N1 A:LG0298 4.5 37.7 1.0
CD A:GLN192 4.5 38.9 1.0
C20 A:LG0298 4.6 40.6 1.0
CG A:GLN192 4.7 35.3 1.0
NH2 A:ARG143 4.7 38.7 1.0
O A:GLU146 4.9 38.1 1.0

Fluorine binding site 3 out of 3 in 3cs7

Go back to Fluorine Binding Sites List in 3cs7
Fluorine binding site 3 out of 3 in the Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Factor Xa in Complex with the Inhibitor 1-(4-Methoxyphenyl)- 6-(4-(1-(Pyrrolidin-1-Ylmethyl)Cyclopropyl)Phenyl)-3- (Trifluoromethyl)-5,6-Dihydro-1H-Pyrazolo[3,4-C]Pyridin- 7(4H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F298

b:43.4
occ:1.00
 F3 A:LG0298 0.0 43.4 1.0
C11 A:LG0298 1.3 42.8 1.0
F1 A:LG0298 2.2 43.7 1.0
F2 A:LG0298 2.2 42.2 1.0
C10 A:LG0298 2.3 41.1 1.0
C12 A:LG0298 3.1 40.0 1.0
N6 A:LG0298 3.3 38.8 1.0
CG A:GLU146 3.4 42.2 1.0
C19 A:LG0298 3.6 41.1 1.0
CD A:GLU146 3.9 43.5 1.0
OE2 A:GLU146 4.0 46.6 1.0
CA A:GLY218 4.1 34.7 1.0
C13 A:LG0298 4.3 40.0 1.0
SG A:CYS220 4.3 33.2 1.0
N1 A:LG0298 4.3 37.7 1.0
O A:GLU146 4.3 38.1 1.0
C A:GLY218 4.6 34.0 1.0
NH1 A:ARG143 4.6 39.1 1.0
OE1 A:GLU146 4.6 43.4 1.0
C20 A:LG0298 4.6 40.6 1.0
CB A:GLU146 4.7 38.2 1.0
N A:GLY218 4.8 31.8 1.0
N A:CYS220 4.9 34.7 1.0

Reference:

J.X.Qiao, D.L.Cheney, R.S.Alexander, A.M.Smallwood, S.R.King, K.He, A.R.Rendina, J.M.Luettgen, R.M.Knabb, R.R.Wexler, P.Y.Lam. Achieving Structural Diversity Using the Perpendicular Conformation of Alpha-Substituted Phenylcyclopropanes to Mimic the Bioactive Conformation of Ortho-Substituted Biphenyl P4 Moieties: Discovery of Novel, Highly Potent Inhibitors of Factor Xa. Bioorg.Med.Chem.Lett. V. 18 4118 2008.
ISSN: ISSN 0960-894X
PubMed: 18550370
DOI: 10.1016/J.BMCL.2008.05.095
Page generated: Wed Jul 31 17:35:20 2024

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