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Calcium in PDB 1wu1: Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine

Enzymatic activity of Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine

All present enzymatic activity of Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine, PDB code: 1wu1 was solved by M.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.569, 72.487, 79.020, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23.5

Other elements in 1wu1:

The structure of Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine (pdb code 1wu1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine, PDB code: 1wu1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1wu1

Go back to Calcium Binding Sites List in 1wu1
Calcium binding site 1 out of 2 in the Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca261

b:52.3
occ:1.00
 OE2 A:GLU77 2.1 78.0 1.0
OD1 A:ASP70 2.2 49.4 1.0
O A:HOH355 2.3 60.1 1.0
OE2 A:GLU80 2.3 68.2 1.0
O A:ASN72 2.5 53.4 1.0
O A:GLN75 2.6 80.3 1.0
CD A:GLU77 3.0 80.5 1.0
CD A:GLU80 3.1 64.1 1.0
CG A:ASP70 3.4 48.5 1.0
C A:GLN75 3.4 80.4 1.0
OE1 A:GLU80 3.5 63.7 1.0
C A:ASN72 3.6 53.5 1.0
CG A:GLU77 3.6 80.8 1.0
N A:GLU77 3.7 79.8 1.0
CA A:GLU76 3.7 81.1 1.0
OE1 A:GLU77 3.9 80.4 1.0
OD2 A:ASP70 3.9 52.1 1.0
N A:GLU76 4.0 81.0 1.0
N A:ASN72 4.1 46.9 1.0
CG A:GLU80 4.1 60.7 1.0
C A:GLU76 4.2 80.2 1.0
CA A:THR73 4.3 59.5 1.0
N A:THR73 4.4 56.1 1.0
CA A:ASN72 4.4 49.9 1.0
CB A:ASP70 4.6 45.2 1.0
CB A:ASN72 4.6 50.2 1.0
CA A:GLN75 4.6 79.4 1.0
N A:ARG71 4.6 41.9 1.0
C A:THR73 4.7 64.3 1.0
N A:GLN75 4.7 77.9 1.0
CB A:GLU77 4.7 80.4 1.0
CA A:ASP70 4.7 42.6 1.0
CA A:GLU77 4.8 79.9 1.0
CB A:GLU76 4.9 81.8 1.0
CG A:GLN75 5.0 80.3 1.0

Calcium binding site 2 out of 2 in 1wu1

Go back to Calcium Binding Sites List in 1wu1
Calcium binding site 2 out of 2 in the Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Factor Xa in Complex with the Inhibitor 4-[(5-Chloroindol-2-Yl) Sulfonyl]-2-(2-Methylpropyl)-1-[[5-(Pyridin-4-Yl) Pyrimidin-2- Yl]Carbonyl]Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca262

b:85.3
occ:1.00
 O A:TYR185 2.2 47.4 1.0
O A:LYS224 2.3 48.9 1.0
O A:HOH367 2.5 58.8 1.0
O A:ARG222 2.5 51.0 1.0
O A:HOH337 2.9 50.5 1.0
O A:ASP185A 3.0 59.7 1.0
C A:TYR185 3.3 49.2 1.0
C A:LYS224 3.5 49.4 1.0
C A:ASP185A 3.6 57.5 1.0
C A:ARG222 3.6 50.4 1.0
N A:LYS224 3.9 51.0 1.0
CA A:ASP185A 3.9 57.6 1.0
O A:HOH322 4.0 50.7 1.0
N A:ASP185A 4.1 55.1 1.0
C A:ALA221 4.1 45.6 1.0
CA A:LYS224 4.2 49.2 1.0
N A:ARG222 4.3 47.0 1.0
O A:ALA221 4.3 46.8 1.0
N A:GLY223A 4.3 51.3 1.0
CA A:TYR185 4.4 46.1 1.0
CA A:ALA221 4.4 45.2 1.0
N A:THR185B 4.4 56.5 1.0
CA A:LYS223 4.4 51.6 1.0
O A:LYS186 4.5 57.8 1.0
N A:LYS223 4.5 49.8 1.0
N A:TYR185 4.5 45.3 1.0
N A:TYR225 4.5 50.1 1.0
CA A:ARG222 4.6 48.3 1.0
C A:LYS223 4.6 50.8 1.0
CB A:LYS224 4.7 48.5 1.0
CA A:TYR225 4.7 48.3 1.0
CB A:TYR185 4.7 43.9 1.0
CA A:THR185B 4.8 58.0 1.0
C A:GLY223A 4.9 53.6 1.0

Reference:

S.Komoriya, N.Haginoya, S.Kobayashi, T.Nagata, A.Mochizuki, M.Suzuki, T.Yoshino, H.Horino, T.Nagahara, M.Suzuki, Y.Isobe, T.Furugoori. Design, Synthesis, and Biological Activity of Non-Basic Compounds As Factor Xa Inhibitors: Sar Study of S1 and Aryl Binding Sites Bioorg.Med.Chem. V. 13 3927 2005.
ISSN: ISSN 0968-0896
PubMed: 15911309
DOI: 10.1016/J.BMC.2005.04.006
Page generated: Fri Jul 12 07:19:09 2024

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