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Chlorine 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:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total only one binding site of Chlorine was 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:

Chlorine binding site 1 out of 1 in 2d1j

Go back to Chlorine Binding Sites List in 2d1j
Chlorine binding site 1 out of 1 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 Chlorine with other atoms in the Cl 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:Cl700

b:36.2
occ:1.00
 CL1 A:D01700 0.0 36.2 1.0
C4 A:D01700 1.7 36.1 1.0
C3 A:D01700 2.7 37.0 1.0
C5 A:D01700 2.7 35.9 1.0
CZ A:TYR228 3.5 27.8 1.0
OH A:TYR228 3.6 27.6 1.0
CG1 A:VAL213 3.6 27.9 1.0
CA A:GLY226 3.6 29.3 1.0
O A:ILE227 3.7 26.1 1.0
O A:TRP215 3.7 35.2 1.0
N A:ILE227 3.7 29.6 1.0
CE2 A:TYR228 3.8 28.4 1.0
CE1 A:TYR228 3.8 28.9 1.0
CB A:ALA190 3.8 33.1 1.0
C A:GLY226 4.0 29.6 1.0
C6 A:D01700 4.0 36.3 1.0
C2 A:D01700 4.0 37.0 1.0
C A:ILE227 4.3 29.0 1.0
O A:HOH302 4.3 27.2 1.0
C A:TRP215 4.3 35.3 1.0
N A:SER214 4.3 31.3 1.0
N A:TRP215 4.4 34.7 1.0
CD2 A:TYR228 4.4 27.8 1.0
CD1 A:TYR228 4.4 27.5 1.0
C1 A:D01700 4.5 36.7 1.0
CA A:VAL213 4.6 27.7 1.0
CA A:ILE227 4.7 29.7 1.0
CG A:TYR228 4.7 28.9 1.0
CB A:VAL213 4.7 26.4 1.0
OD1 A:ASP189 4.7 39.5 1.0
CA A:TRP215 4.8 36.0 1.0
C A:VAL213 4.9 29.9 1.0
O A:GLY226 5.0 28.6 1.0
N A:GLY226 5.0 33.2 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: Sat Dec 12 09:02:47 2020

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