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Fluorine in PDB 3m35: Trypsin 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 Trypsin 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 Trypsin in Complex with the Inhibitor 1-[3-(Aminomethyl) Phenyl]-N-[3-Fluoro-2'-(Methylsulfonyl)Biphenyl-4-Yl]-3- (Trifluoromethyl)-1H-Pyrazole-5-Carboxamide (DPC423):
3.4.21.4;

Protein crystallography data

The structure of Trypsin 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: 3m35 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) 19.41 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.400, 64.000, 69.300, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 23.4

Other elements in 3m35:

The structure of Trypsin 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 Trypsin 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 3m35). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Trypsin 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: 3m35:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3m35

Go back to Fluorine Binding Sites List in 3m35
Fluorine binding site 1 out of 4 in the Trypsin 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 Trypsin 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:40.2
occ:1.00
 F1 A:M35301 0.0 40.2 1.0
C11 A:M35301 1.3 40.5 1.0
F3 A:M35301 2.1 40.1 1.0
F2 A:M35301 2.2 40.0 1.0
C10 A:M35301 2.3 40.8 1.0
C12 A:M35301 3.1 41.5 1.0
N6 A:M35301 3.3 40.9 1.0
CA A:GLY219 3.8 17.1 1.0
SG A:CYS220 4.2 18.9 1.0
C13 A:M35301 4.2 42.1 1.0
N1 A:M35301 4.3 41.1 1.0
C A:GLY219 4.4 17.1 1.0
N A:GLY219 4.6 17.7 1.0
N A:CYS220 4.7 17.1 1.0
O A:GLY219 4.9 16.2 1.0
O A:HOH444 5.0 29.1 1.0

Fluorine binding site 2 out of 4 in 3m35

Go back to Fluorine Binding Sites List in 3m35
Fluorine binding site 2 out of 4 in the Trypsin 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 Trypsin 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:40.0
occ:1.00
 F2 A:M35301 0.0 40.0 1.0
C11 A:M35301 1.3 40.5 1.0
F3 A:M35301 2.1 40.1 1.0
F1 A:M35301 2.2 40.2 1.0
C10 A:M35301 2.4 40.8 1.0
N6 A:M35301 2.8 40.9 1.0
NE2 A:GLN192 3.1 27.4 1.0
CD A:GLN192 3.2 27.1 1.0
CG A:GLN192 3.7 24.9 1.0
OE1 A:GLN192 3.7 28.8 1.0
C12 A:M35301 3.7 41.5 1.0
SG A:CYS191 3.8 18.9 1.0
CB A:GLN192 3.8 20.4 1.0
SG A:CYS220 4.0 18.9 1.0
N1 A:M35301 4.2 41.1 1.0
N A:GLN192 4.4 18.3 1.0
C13 A:M35301 4.6 42.1 1.0
ND2 A:ASN143 4.8 22.0 1.0
CA A:GLN192 4.8 18.6 1.0

Fluorine binding site 3 out of 4 in 3m35

Go back to Fluorine Binding Sites List in 3m35
Fluorine binding site 3 out of 4 in the Trypsin 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 Trypsin 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:40.1
occ:1.00
 F3 A:M35301 0.0 40.1 1.0
C11 A:M35301 1.3 40.5 1.0
F2 A:M35301 2.1 40.0 1.0
F1 A:M35301 2.1 40.2 1.0
C10 A:M35301 2.3 40.8 1.0
C12 A:M35301 3.0 41.5 1.0
N6 A:M35301 3.5 40.9 1.0
OE1 A:GLN192 3.9 28.8 1.0
CD A:GLN192 4.1 27.1 1.0
NE2 A:GLN192 4.1 27.4 1.0
C13 A:M35301 4.3 42.1 1.0
N1 A:M35301 4.5 41.1 1.0
CB A:GLN192 4.9 20.4 1.0
CG A:GLN192 4.9 24.9 1.0

Fluorine binding site 4 out of 4 in 3m35

Go back to Fluorine Binding Sites List in 3m35
Fluorine binding site 4 out of 4 in the Trypsin 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 Trypsin 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:47.7
occ:1.00
 F4 A:M35301 0.0 47.7 1.0
C44 A:M35301 1.3 47.5 1.0
C14 A:M35301 2.4 48.9 1.0
C7 A:M35301 2.4 47.0 1.0
N5 A:M35301 2.8 45.4 1.0
O A:HOH433 3.0 18.4 1.0
O3 A:M35301 3.1 43.1 1.0
C8 A:M35301 3.2 43.4 1.0
O A:HOH499 3.6 34.1 1.0
C16 A:M35301 3.7 50.3 1.0
C22 A:M35301 3.7 47.4 1.0
CB A:TRP215 4.0 10.3 1.0
C18 A:M35301 4.2 49.0 1.0
C13 A:M35301 4.3 42.1 1.0
CA A:TRP215 4.9 11.1 1.0
C17 A:M35301 5.0 51.8 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: Sun Dec 13 11:50:48 2020

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