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Fluorine in PDB 3m37: Factor Xa in Complex with the Inhibitor 1-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602)

Enzymatic activity of Factor Xa in Complex with the Inhibitor 1-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602)

All present enzymatic activity of Factor Xa in Complex with the Inhibitor 1-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602):
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor 1-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602), PDB code: 3m37 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) 25.16 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.100, 72.200, 78.700, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 26.3

Other elements in 3m37:

The structure of Factor Xa in Complex with the Inhibitor 1-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602) 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-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602) (pdb code 3m37). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Factor Xa in Complex with the Inhibitor 1-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602), PDB code: 3m37:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3m37

Go back to Fluorine Binding Sites List in 3m37
Fluorine binding site 1 out of 4 in the Factor Xa in Complex with the Inhibitor 1-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602)


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-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:22.9
occ:1.00
 F1 A:M37301 0.0 22.9 1.0
C11 A:M37301 1.3 20.9 1.0
F2 A:M37301 2.2 21.2 1.0
F3 A:M37301 2.2 19.1 1.0
C10 A:M37301 2.3 20.8 1.0
C12 A:M37301 2.9 21.3 1.0
O A:HOH504 3.4 32.0 1.0
N6 A:M37301 3.4 20.8 1.0
NH1 A:ARG143 3.7 20.9 1.0
OE1 A:GLN192 4.1 25.2 1.0
C13 A:M37301 4.2 19.8 1.0
N1 A:M37301 4.4 19.2 1.0
O A:GLU146 4.5 22.0 1.0
CB A:GLN192 4.6 17.2 1.0
CZ A:ARG143 4.7 21.8 1.0
CG A:GLU146 4.8 28.1 1.0
CG A:GLN192 5.0 20.5 1.0
CD A:GLN192 5.0 24.7 1.0
O A:HOH492 5.0 25.2 1.0

Fluorine binding site 2 out of 4 in 3m37

Go back to Fluorine Binding Sites List in 3m37
Fluorine binding site 2 out of 4 in the Factor Xa in Complex with the Inhibitor 1-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602)


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-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:21.2
occ:1.00
 F2 A:M37301 0.0 21.2 1.0
C11 A:M37301 1.3 20.9 1.0
F3 A:M37301 2.1 19.1 1.0
F1 A:M37301 2.2 22.9 1.0
C10 A:M37301 2.3 20.8 1.0
C12 A:M37301 3.1 21.3 1.0
CG A:GLU146 3.1 28.1 1.0
N6 A:M37301 3.3 20.8 1.0
CD A:GLU146 3.7 30.7 1.0
SG A:CYS220 3.8 19.4 1.0
CA A:GLY218 3.9 17.7 1.0
O A:HOH504 3.9 32.0 1.0
OE1 A:GLU146 4.0 32.5 1.0
C A:GLY218 4.3 18.8 1.0
C13 A:M37301 4.3 19.8 1.0
O A:GLU146 4.3 22.0 1.0
N1 A:M37301 4.4 19.2 1.0
N A:CYS220 4.4 17.8 1.0
CB A:GLU146 4.4 26.1 1.0
OE2 A:GLU146 4.4 30.5 1.0
N A:GLY218 4.6 17.4 1.0
CA A:GLU146 4.7 23.6 1.0
O A:HOH492 4.7 25.2 1.0
C A:GLU146 4.9 23.9 1.0
NH1 A:ARG143 4.9 20.9 1.0
O A:GLY218 5.0 18.9 1.0
SG A:CYS191 5.0 19.8 1.0

Fluorine binding site 3 out of 4 in 3m37

Go back to Fluorine Binding Sites List in 3m37
Fluorine binding site 3 out of 4 in the Factor Xa in Complex with the Inhibitor 1-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602)


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-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:19.1
occ:1.00
 F3 A:M37301 0.0 19.1 1.0
C11 A:M37301 1.3 20.9 1.0
F2 A:M37301 2.1 21.2 1.0
F1 A:M37301 2.2 22.9 1.0
C10 A:M37301 2.3 20.8 1.0
N6 A:M37301 2.7 20.8 1.0
NH1 A:ARG143 3.4 20.9 1.0
O A:GLU146 3.4 22.0 1.0
CB A:GLN192 3.6 17.2 1.0
SG A:CYS220 3.6 19.4 1.0
SG A:CYS191 3.6 19.8 1.0
C12 A:M37301 3.7 21.3 1.0
O A:HOH504 4.0 32.0 1.0
CG A:GLU146 4.0 28.1 1.0
N A:GLN192 4.1 14.5 1.0
N1 A:M37301 4.1 19.2 1.0
C A:GLU146 4.3 23.9 1.0
CA A:GLU146 4.3 23.6 1.0
CZ A:ARG143 4.3 21.8 1.0
CD A:ARG143 4.4 17.9 1.0
CA A:GLN192 4.4 13.9 1.0
C13 A:M37301 4.5 19.8 1.0
CG A:GLN192 4.6 20.5 1.0
OE1 A:GLN192 4.6 25.2 1.0
NE A:ARG143 4.7 20.3 1.0
CB A:GLU146 4.8 26.1 1.0

Fluorine binding site 4 out of 4 in 3m37

Go back to Fluorine Binding Sites List in 3m37
Fluorine binding site 4 out of 4 in the Factor Xa in Complex with the Inhibitor 1-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Factor Xa in Complex with the Inhibitor 1-[2-(Aminomethyl) Phenyl]-N-(3-Fluoro-2'-Sulfamoylbiphenyl-4-Yl)-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC602) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:24.6
occ:1.00
 F4 A:M37301 0.0 24.6 1.0
C44 A:M37301 1.3 20.4 1.0
C14 A:M37301 2.4 20.4 1.0
C7 A:M37301 2.4 19.8 1.0
O3 A:M37301 2.8 17.3 1.0
N5 A:M37301 2.8 18.6 1.0
C8 A:M37301 3.0 19.5 1.0
O A:HOH452 3.1 18.4 1.0
O A:HOH499 3.2 24.7 1.0
OH A:TYR99 3.4 26.9 1.0
CZ A:TYR99 3.6 24.2 1.0
C16 A:M37301 3.7 20.0 1.0
C22 A:M37301 3.7 19.0 1.0
CE2 A:TYR99 3.9 23.1 1.0
CB A:TRP215 4.0 13.2 1.0
C13 A:M37301 4.2 19.8 1.0
C18 A:M37301 4.2 20.1 1.0
CE1 A:TYR99 4.3 22.6 1.0
N2 A:M37301 4.5 28.9 1.0
CD2 A:TYR99 4.8 21.0 1.0
C17 A:M37301 4.9 20.9 1.0
CA A:TRP215 4.9 12.6 1.0
C12 A:M37301 5.0 21.3 1.0

Reference:

J.R.Pruitt, D.J.P.Pinto, R.A.Jr.Galemmo, R.S.Alexander, K.A.Rossi, B.L.Wells, S.Drummond, L.L.Bostrom, D.Burdick, R.Bruckner, H.Chen, A.Smallwood, P.C.Wong, M.R.Wright, S.Bai, J.M.Luettgen, R.M.Knabb, P.Y.S.Lam, R.R.Wexler. Discovery of 1-(2-Aminomethylphenyl)-3-Trifluoromethyl-N-[3- Fluoro-2'-(Aminosulfonyl)[1,1'-Biphenyl)]-1H- Pyrazole-5-Carboxyamide (DPC602), A Potent, Selective, and Orally Bioavailable Factor Xa Inhibitor. J.Med.Chem. V. 46 5298 2003.
ISSN: ISSN 0022-2623
PubMed: 14640539
Page generated: Wed Jul 31 20:39:35 2024

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