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Fluorine in PDB 3m36: Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423)

Enzymatic activity of Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423)

All present enzymatic activity of Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423):
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423), PDB code: 3m36 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) 19.74 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.800, 72.300, 77.700, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.4

Other elements in 3m36:

The structure of Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423) 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-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423) (pdb code 3m36). 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-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423), PDB code: 3m36:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3m36

Go back to Fluorine Binding Sites List in 3m36
Fluorine binding site 1 out of 4 in the Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423)


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-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:30.9
occ:1.00
 F1 A:M35301 0.0 30.9 1.0
C11 A:M35301 1.3 30.4 1.0
F2 A:M35301 2.1 33.7 1.0
F3 A:M35301 2.2 29.4 1.0
C10 A:M35301 2.3 30.7 1.0
C12 A:M35301 3.0 28.8 1.0
NH1 A:ARG143 3.4 35.7 1.0
N6 A:M35301 3.5 28.5 1.0
CZ A:ARG143 4.2 36.8 1.0
OE1 A:GLN192 4.2 44.3 1.0
C13 A:M35301 4.3 29.4 1.0
CB A:GLN192 4.4 30.3 1.0
O A:GLU146 4.4 39.2 1.0
N1 A:M35301 4.5 27.3 1.0
CG A:GLN192 4.6 36.9 1.0
NH2 A:ARG143 4.7 37.9 1.0
CD A:GLN192 4.9 41.6 1.0

Fluorine binding site 2 out of 4 in 3m36

Go back to Fluorine Binding Sites List in 3m36
Fluorine binding site 2 out of 4 in the Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423)


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-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:33.7
occ:1.00
 F2 A:M35301 0.0 33.7 1.0
C11 A:M35301 1.3 30.4 1.0
F3 A:M35301 2.1 29.4 1.0
F1 A:M35301 2.1 30.9 1.0
C10 A:M35301 2.3 30.7 1.0
C12 A:M35301 3.0 28.8 1.0
N6 A:M35301 3.3 28.5 1.0
CA A:GLY218 3.9 29.2 1.0
OE2 A:GLU146 3.9 39.0 1.0
CD A:GLU146 4.1 39.7 1.0
CB A:GLU146 4.1 38.7 1.0
CG A:GLU146 4.2 39.1 1.0
C13 A:M35301 4.2 29.4 1.0
N1 A:M35301 4.3 27.3 1.0
SG A:CYS220 4.4 31.9 1.0
O A:GLU146 4.4 39.2 1.0
C A:GLY218 4.5 30.6 1.0
CA A:GLU146 4.5 38.1 1.0
O A:HOH480 4.6 24.1 1.0
N A:GLY218 4.6 27.9 1.0
NH1 A:ARG143 4.7 35.7 1.0
C A:GLU146 4.9 39.3 1.0
OE1 A:GLU146 4.9 40.1 1.0
N A:CYS220 4.9 30.6 1.0

Fluorine binding site 3 out of 4 in 3m36

Go back to Fluorine Binding Sites List in 3m36
Fluorine binding site 3 out of 4 in the Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423)


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-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:29.4
occ:1.00
 F3 A:M35301 0.0 29.4 1.0
C11 A:M35301 1.3 30.4 1.0
F2 A:M35301 2.1 33.7 1.0
F1 A:M35301 2.2 30.9 1.0
C10 A:M35301 2.3 30.7 1.0
N6 A:M35301 2.7 28.5 1.0
NH1 A:ARG143 3.4 35.7 1.0
O A:GLU146 3.5 39.2 1.0
SG A:CYS191 3.6 24.2 1.0
CB A:GLN192 3.6 30.3 1.0
C12 A:M35301 3.6 28.8 1.0
SG A:CYS220 3.8 31.9 1.0
CA A:GLU146 3.9 38.1 1.0
N1 A:M35301 4.0 27.3 1.0
C A:GLU146 4.1 39.3 1.0
CD A:ARG143 4.2 34.7 1.0
N A:GLN192 4.3 25.4 1.0
CZ A:ARG143 4.3 36.8 1.0
CB A:GLU146 4.3 38.7 1.0
C13 A:M35301 4.5 29.4 1.0
CG A:GLN192 4.5 36.9 1.0
CG A:GLU146 4.6 39.1 1.0
NE A:ARG143 4.6 36.5 1.0
CA A:GLN192 4.6 26.2 1.0
OE1 A:GLN192 4.7 44.3 1.0

Fluorine binding site 4 out of 4 in 3m36

Go back to Fluorine Binding Sites List in 3m36
Fluorine binding site 4 out of 4 in the Factor Xa in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423)


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-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:36.8
occ:1.00
 F4 A:M35301 0.0 36.8 1.0
C44 A:M35301 1.3 31.8 1.0
C7 A:M35301 2.3 30.6 1.0
C14 A:M35301 2.4 33.3 1.0
N5 A:M35301 2.7 30.4 1.0
O3 A:M35301 2.9 29.4 1.0
C8 A:M35301 3.1 28.8 1.0
O A:HOH434 3.2 27.6 1.0
OH A:TYR99 3.5 29.1 1.0
CZ A:TYR99 3.6 29.9 1.0
C22 A:M35301 3.6 29.6 1.0
CE2 A:TYR99 3.7 29.6 1.0
C16 A:M35301 3.7 34.0 1.0
CB A:TRP215 4.0 23.1 1.0
C18 A:M35301 4.1 31.9 1.0
C13 A:M35301 4.3 29.4 1.0
CE1 A:TYR99 4.3 30.8 1.0
CD2 A:TYR99 4.5 29.5 1.0
C9 A:M35301 4.9 38.9 1.0
CA A:TRP215 5.0 23.8 1.0
C17 A:M35301 5.0 35.2 1.0
CG A:TRP215 5.0 24.3 1.0
CD1 A:TYR99 5.0 29.8 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: Mon Jul 14 17:52:11 2025

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