Fluorine in PDB 2xc0: Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor

All present enzymatic activity of Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor:
3.4.21.6;

The structure of Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor, PDB code: 2xc0 was solved by D.W.Banner, J.Benz, D.Schlatter, L.Anselm, W.Haap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.54 / 2.05
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.410, 105.410, 50.950, 90.00, 90.00, 90.00
R / Rfree (%)	18.41 / 24.008

The structure of Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Sodium	(Na)	1 atom

The binding sites of Fluorine atom in the Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor (pdb code 2xc0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor, PDB code: 2xc0:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor


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 A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1246 b:25.8 occ:1.00 F34 A:8NC1246 0.0 25.8 1.0 C16 A:8NC1246 1.4 23.7 1.0 C15 A:8NC1246 2.3 24.8 1.0 C13 A:8NC1246 2.4 21.9 1.0 N12 A:8NC1246 2.6 28.6 1.0 O A:HOH2065 3.0 51.5 1.0 OH A:TYR99 3.4 26.6 1.0 CZ A:TYR99 3.5 26.1 1.0 C29 A:8NC1246 3.6 23.5 1.0 C11 A:8NC1246 3.6 21.4 1.0 CE2 A:TYR99 3.6 21.8 1.0 C5 A:8NC1246 3.8 33.7 1.0 CB A:TRP215 3.9 21.9 1.0 C28 A:8NC1246 4.1 23.4 1.0 O A:HOH2146 4.1 32.8 1.0 CE1 A:TYR99 4.2 24.9 1.0 CD2 A:TYR99 4.4 22.7 1.0 O23 A:8NC1246 4.5 43.6 1.0 O A:HOH2066 4.5 41.0 1.0 C2 A:8NC1246 4.6 34.3 1.0 N6 A:8NC1246 4.8 21.7 1.0 CA A:TRP215 4.8 21.1 1.0 O24 A:8NC1246 4.9 41.4 1.0 CD1 A:TYR99 4.9 23.1 1.0 O A:SER214 4.9 20.9 1.0 O27 A:8NC1246 5.0 23.0 1.0 CG A:TRP215 5.0 21.8 1.0 CG A:TYR99 5.0 22.6 1.0

Fluorine binding site 2 out of 2 in the Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor


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 A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1246 b:31.6 occ:1.00 F35 A:8NC1246 0.0 31.6 1.0 C17 A:8NC1246 1.4 29.7 1.0 C26 A:8NC1246 2.4 27.5 1.0 C18 A:8NC1246 2.4 27.5 1.0 O37 A:8NC1246 2.7 27.6 1.0 CG1 A:VAL213 3.1 22.1 1.0 O A:HOH2146 3.3 32.8 1.0 O A:SER214 3.5 20.9 1.0 OG A:SER195 3.5 31.3 1.0 C A:SER214 3.6 21.3 1.0 C32 A:8NC1246 3.7 26.9 1.0 C22 A:8NC1246 3.7 28.4 1.0 N A:TRP215 3.7 21.2 1.0 CA A:SER195 3.8 23.5 1.0 CB A:SER195 3.9 25.3 1.0 N A:SER195 3.9 23.9 1.0 CA A:TRP215 3.9 21.1 1.0 O A:CYS191 3.9 25.9 1.0 N A:SER214 4.0 19.5 1.0 C38 A:8NC1246 4.1 26.8 1.0 C36 A:8NC1246 4.1 25.2 1.0 C A:VAL213 4.2 20.8 1.0 CA A:SER214 4.3 20.5 1.0 C A:CYS191 4.3 27.1 1.0 CB A:VAL213 4.4 20.4 1.0 O24 A:8NC1246 4.4 41.4 1.0 C A:TRP215 4.5 20.6 1.0 O A:VAL213 4.5 20.0 1.0 C A:ASP194 4.7 25.5 1.0 CA A:VAL213 4.8 20.7 1.0 N A:GLN192 4.8 29.7 1.0 N14 A:8NC1246 4.8 31.2 1.0 O A:TRP215 4.9 22.4 1.0 N A:CYS191 4.9 29.5 1.0 CA A:CYS191 5.0 29.6 1.0 CB A:ALA190 5.0 27.7 1.0

L.Anselm, D.W.Banner, J.Benz, K.Groebke Zbinden, J.Himber, H.Hilpert, W.Huber, B.Kuhn, J.L.Mary, M.B.Otteneder, N.Panday, F.Ricklin, M.Stahl, S.Thomi, W.Haap. Discovery of A Factor Xa Inhibitor (3R,4R)-1-(2,2-Difluoro-Ethyl)-Pyrrolidine-3,4-Dicarboxylic Acid 3-[(5-Chloro-Pyridin-2-Yl)-Amide] 4-{[2-Fluoro-4-(2-Oxo-2H-Pyridin-1-Yl)-Phenyl]-Amide} As A Clinical Candidate. Bioorg.Med.Chem. V. 20 5313 2010.
ISSN: ISSN 0968-0896
PubMed: 20650636
DOI: 10.1016/J.BMCL.2010.06.126