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Fluorine in PDB 2xc4: Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor

Enzymatic activity of 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;

Protein crystallography data

The structure of Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor, PDB code: 2xc4 was solved by D.W.Banner, J.Benz, D.Schlatter, S.Thomi, W.Haap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.49 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.840, 74.550, 76.800, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.4

Other elements in 2xc4:

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
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor (pdb code 2xc4). 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 A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor, PDB code: 2xc4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 2xc4

Go back to Fluorine Binding Sites List in 2xc4
Fluorine binding site 1 out of 4 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:24.9
occ:1.00
 F32 A:IVK1246 0.0 24.9 1.0
C24 A:IVK1246 1.4 21.5 1.0
C19 A:IVK1246 2.4 21.4 1.0
C22 A:IVK1246 2.4 22.3 1.0
N8 A:IVK1246 2.7 23.7 1.0
O9 A:IVK1246 2.8 19.8 1.0
C7 A:IVK1246 2.9 22.9 1.0
O A:HOH2102 3.0 23.5 1.0
O A:HOH2236 3.0 40.1 1.0
O A:HOH2212 3.4 25.7 1.0
OH A:TYR99 3.4 20.2 1.0
CZ A:TYR99 3.5 21.1 1.0
CE2 A:TYR99 3.6 20.4 1.0
C20 A:IVK1246 3.6 22.5 1.0
C21 A:IVK1246 3.6 22.8 1.0
CB A:TRP215 3.9 14.6 1.0
C23 A:IVK1246 4.1 21.5 1.0
C2 A:IVK1246 4.1 21.9 1.0
CE1 A:TYR99 4.3 20.4 1.0
CD2 A:TYR99 4.4 17.6 1.0
O A:HOH2238 4.7 32.6 1.0
CA A:TRP215 4.7 13.7 1.0
N25 A:IVK1246 4.8 24.0 1.0
C3 A:IVK1246 4.9 22.3 1.0
CG A:TRP215 4.9 15.1 1.0

Fluorine binding site 2 out of 4 in 2xc4

Go back to Fluorine Binding Sites List in 2xc4
Fluorine binding site 2 out of 4 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:34.6
occ:1.00
 F35 A:IVK1246 0.0 34.6 1.0
C34 A:IVK1246 1.4 34.3 1.0
F30 A:IVK1246 2.3 32.8 1.0
F36 A:IVK1246 2.3 38.9 1.0
C33 A:IVK1246 2.4 29.6 1.0
O A:HOH2146 3.4 44.5 1.0
NH1 A:ARG143 3.6 28.8 1.0
N4 A:IVK1246 3.6 26.2 1.0
O A:GLU147 3.9 22.4 1.0
CZ A:ARG143 4.3 27.4 1.0
C5 A:IVK1246 4.3 23.1 1.0
O A:HOH2145 4.4 42.9 1.0
NZ A:LYS148 4.4 28.3 0.5
CG A:GLU147 4.5 24.4 1.0
CD A:LYS148 4.6 27.9 0.5
NH2 A:ARG143 4.7 29.3 1.0
C3 A:IVK1246 4.8 22.3 1.0
C A:GLU147 4.8 23.3 1.0

Fluorine binding site 3 out of 4 in 2xc4

Go back to Fluorine Binding Sites List in 2xc4
Fluorine binding site 3 out of 4 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 3 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:38.9
occ:1.00
 F36 A:IVK1246 0.0 38.9 1.0
C34 A:IVK1246 1.4 34.3 1.0
F30 A:IVK1246 2.3 32.8 1.0
F35 A:IVK1246 2.3 34.6 1.0
C33 A:IVK1246 2.4 29.6 1.0
N4 A:IVK1246 2.6 26.2 1.0
C5 A:IVK1246 3.5 23.1 1.0
OE1 A:GLN192 3.6 38.4 1.0
CZ A:ARG143 3.8 27.4 1.0
C3 A:IVK1246 3.9 22.3 1.0
NH1 A:ARG143 3.9 28.8 1.0
CB A:GLN192 3.9 20.4 1.0
CG A:GLN192 3.9 24.9 1.0
NH2 A:ARG143 3.9 29.3 1.0
CD A:GLN192 4.1 31.0 1.0
NE A:ARG143 4.3 25.8 1.0
O A:HOH2145 4.4 42.9 1.0
C2 A:IVK1246 4.8 21.9 1.0
C1 A:IVK1246 4.8 21.9 1.0
O A:HOH2146 4.9 44.5 1.0
O A:GLU147 4.9 22.4 1.0
CD A:ARG143 4.9 24.5 1.0

Fluorine binding site 4 out of 4 in 2xc4

Go back to Fluorine Binding Sites List in 2xc4
Fluorine binding site 4 out of 4 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 4 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:32.8
occ:1.00
 F30 A:IVK1246 0.0 32.8 1.0
C34 A:IVK1246 1.4 34.3 1.0
F36 A:IVK1246 2.3 38.9 1.0
F35 A:IVK1246 2.3 34.6 1.0
C33 A:IVK1246 2.4 29.6 1.0
C5 A:IVK1246 2.8 23.1 1.0
N4 A:IVK1246 2.9 26.2 1.0
O A:GLU147 3.2 22.4 1.0
NH1 A:ARG143 3.6 28.8 1.0
CB A:GLN192 3.8 20.4 1.0
CZ A:ARG143 4.0 27.4 1.0
CD A:ARG143 4.0 24.5 1.0
CG A:GLU147 4.1 24.4 1.0
NE A:ARG143 4.1 25.8 1.0
C A:GLU147 4.2 23.3 1.0
SG A:CYS220 4.2 17.9 1.0
SG A:CYS191 4.2 15.7 1.0
C1 A:IVK1246 4.3 21.9 1.0
C3 A:IVK1246 4.4 22.3 1.0
CA A:GLU147 4.6 23.9 1.0
CG A:GLN192 4.6 24.9 1.0
NH2 A:ARG143 4.7 29.3 1.0
OE1 A:GLN192 4.8 38.4 1.0
N A:GLN192 4.8 15.4 1.0
CA A:GLN192 4.9 18.4 1.0
O A:HOH2146 4.9 44.5 1.0
CB A:GLU147 5.0 23.6 1.0
C2 A:IVK1246 5.0 21.9 1.0

Reference:

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
Page generated: Wed Jul 31 16:37:36 2024

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