Atomistry » Fluorine » PDB 2x2n-2y1w » 2xc4
Atomistry »
  Fluorine »
    PDB 2x2n-2y1w »
      2xc4 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy