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Calcium in PDB 2d1j: Factor Xa in Complex with the Inhibitor 2-[[4-[(5- Chloroindol-2-Yl)Sulfonyl]Piperazin-1-Yl] Carbonyl]Thieno[3,2-B]Pyridine N-Oxide

Enzymatic activity of Factor Xa in Complex with the Inhibitor 2-[[4-[(5- Chloroindol-2-Yl)Sulfonyl]Piperazin-1-Yl] Carbonyl]Thieno[3,2-B]Pyridine N-Oxide

All present enzymatic activity of Factor Xa in Complex with the Inhibitor 2-[[4-[(5- Chloroindol-2-Yl)Sulfonyl]Piperazin-1-Yl] Carbonyl]Thieno[3,2-B]Pyridine N-Oxide:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor 2-[[4-[(5- Chloroindol-2-Yl)Sulfonyl]Piperazin-1-Yl] Carbonyl]Thieno[3,2-B]Pyridine N-Oxide, PDB code: 2d1j 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.078, 73.122, 79.949, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.2

Other elements in 2d1j:

The structure of Factor Xa in Complex with the Inhibitor 2-[[4-[(5- Chloroindol-2-Yl)Sulfonyl]Piperazin-1-Yl] Carbonyl]Thieno[3,2-B]Pyridine N-Oxide 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 2-[[4-[(5- Chloroindol-2-Yl)Sulfonyl]Piperazin-1-Yl] Carbonyl]Thieno[3,2-B]Pyridine N-Oxide (pdb code 2d1j). 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 2-[[4-[(5- Chloroindol-2-Yl)Sulfonyl]Piperazin-1-Yl] Carbonyl]Thieno[3,2-B]Pyridine N-Oxide, PDB code: 2d1j:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2d1j

Go back to Calcium Binding Sites List in 2d1j
Calcium binding site 1 out of 2 in the Factor Xa in Complex with the Inhibitor 2-[[4-[(5- Chloroindol-2-Yl)Sulfonyl]Piperazin-1-Yl] Carbonyl]Thieno[3,2-B]Pyridine N-Oxide


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 2-[[4-[(5- Chloroindol-2-Yl)Sulfonyl]Piperazin-1-Yl] Carbonyl]Thieno[3,2-B]Pyridine N-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca261

b:49.3
occ:1.00
 O A:GLN75 2.0 70.9 1.0
O A:HOH353 2.2 46.6 1.0
OD1 A:ASP70 2.2 42.1 1.0
OE2 A:GLU80 2.3 49.4 1.0
O A:ASN72 2.3 39.4 1.0
O A:HOH342 2.6 46.7 1.0
C A:GLN75 3.2 69.6 1.0
CG A:ASP70 3.4 39.6 1.0
C A:ASN72 3.4 40.0 1.0
CD A:GLU80 3.4 48.5 1.0
OD2 A:ASP70 3.9 40.9 1.0
CG A:GLU80 3.9 45.3 1.0
N A:ASN72 3.9 37.7 1.0
CA A:GLU76 4.0 72.0 1.0
N A:GLU76 4.0 71.3 1.0
N A:GLU77 4.1 72.5 1.0
CA A:ASN72 4.1 39.7 1.0
N A:GLN75 4.2 64.3 1.0
CA A:GLN75 4.3 67.2 1.0
N A:THR73 4.3 40.2 1.0
CA A:THR73 4.3 43.7 1.0
CB A:ASN72 4.4 39.9 1.0
OE1 A:GLU80 4.5 49.5 1.0
N A:ARG71 4.5 35.7 1.0
C A:GLU76 4.6 72.4 1.0
CB A:ASP70 4.6 37.7 1.0
CA A:ASP70 4.6 36.6 1.0
C A:THR73 4.7 48.7 1.0
N A:GLU74 4.9 53.2 1.0
CG A:GLN75 5.0 67.5 1.0

Calcium binding site 2 out of 2 in 2d1j

Go back to Calcium Binding Sites List in 2d1j
Calcium binding site 2 out of 2 in the Factor Xa in Complex with the Inhibitor 2-[[4-[(5- Chloroindol-2-Yl)Sulfonyl]Piperazin-1-Yl] Carbonyl]Thieno[3,2-B]Pyridine N-Oxide


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 2-[[4-[(5- Chloroindol-2-Yl)Sulfonyl]Piperazin-1-Yl] Carbonyl]Thieno[3,2-B]Pyridine N-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca262

b:78.4
occ:1.00
 O A:TYR185 2.1 42.0 1.0
O A:LYS224 2.2 44.2 1.0
O A:ARG222 2.4 52.9 1.0
O A:HOH388 2.5 53.6 1.0
O A:ASP185A 3.1 55.5 1.0
O A:HOH323 3.2 51.0 1.0
C A:TYR185 3.3 43.7 1.0
C A:LYS224 3.4 43.3 1.0
C A:ARG222 3.5 51.7 1.0
C A:ASP185A 3.6 54.4 1.0
N A:LYS224 3.8 46.7 1.0
CA A:ASP185A 4.0 52.9 1.0
N A:ASP185A 4.1 49.4 1.0
C A:ALA221 4.1 44.3 1.0
CA A:LYS224 4.1 44.4 1.0
N A:ARG222 4.2 46.5 1.0
O A:HOH313 4.2 37.0 1.0
O A:ALA221 4.2 43.2 1.0
N A:LYS223 4.3 50.9 1.0
N A:GLY223A 4.3 47.1 1.0
CA A:LYS223 4.3 50.6 1.0
O A:LYS186 4.4 52.8 1.0
N A:TYR225 4.4 42.2 1.0
CA A:TYR185 4.4 41.6 1.0
N A:THR185B 4.5 54.6 1.0
CA A:ARG222 4.5 48.8 1.0
CA A:ALA221 4.5 43.1 1.0
C A:LYS223 4.5 48.5 1.0
N A:TYR185 4.6 40.8 1.0
CA A:TYR225 4.7 39.1 1.0
CB A:LYS224 4.7 45.3 1.0
C A:GLY223A 4.8 48.6 1.0
CB A:TYR185 4.8 41.4 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 09:39:20 2024

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