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Calcium in PDB 1v3x: Factor Xa in Complex with the Inhibitor 1-[6-Methyl-4,5,6,7- Tetrahydrothiazolo(5,4-C)Pyridin-2-Yl] Carbonyl-2- Carbamoyl-4-(6-Chloronaphth-2-Ylsulphonyl)Piperazine

Enzymatic activity of Factor Xa in Complex with the Inhibitor 1-[6-Methyl-4,5,6,7- Tetrahydrothiazolo(5,4-C)Pyridin-2-Yl] Carbonyl-2- Carbamoyl-4-(6-Chloronaphth-2-Ylsulphonyl)Piperazine

All present enzymatic activity of Factor Xa in Complex with the Inhibitor 1-[6-Methyl-4,5,6,7- Tetrahydrothiazolo(5,4-C)Pyridin-2-Yl] Carbonyl-2- Carbamoyl-4-(6-Chloronaphth-2-Ylsulphonyl)Piperazine:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor 1-[6-Methyl-4,5,6,7- Tetrahydrothiazolo(5,4-C)Pyridin-2-Yl] Carbonyl-2- Carbamoyl-4-(6-Chloronaphth-2-Ylsulphonyl)Piperazine, PDB code: 1v3x 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 (°) 56.050, 71.927, 78.799, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.3

Other elements in 1v3x:

The structure of Factor Xa in Complex with the Inhibitor 1-[6-Methyl-4,5,6,7- Tetrahydrothiazolo(5,4-C)Pyridin-2-Yl] Carbonyl-2- Carbamoyl-4-(6-Chloronaphth-2-Ylsulphonyl)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 1-[6-Methyl-4,5,6,7- Tetrahydrothiazolo(5,4-C)Pyridin-2-Yl] Carbonyl-2- Carbamoyl-4-(6-Chloronaphth-2-Ylsulphonyl)Piperazine (pdb code 1v3x). 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 1-[6-Methyl-4,5,6,7- Tetrahydrothiazolo(5,4-C)Pyridin-2-Yl] Carbonyl-2- Carbamoyl-4-(6-Chloronaphth-2-Ylsulphonyl)Piperazine, PDB code: 1v3x:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1v3x

Go back to Calcium Binding Sites List in 1v3x
Calcium binding site 1 out of 2 in the Factor Xa in Complex with the Inhibitor 1-[6-Methyl-4,5,6,7- Tetrahydrothiazolo(5,4-C)Pyridin-2-Yl] Carbonyl-2- Carbamoyl-4-(6-Chloronaphth-2-Ylsulphonyl)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 1-[6-Methyl-4,5,6,7- Tetrahydrothiazolo(5,4-C)Pyridin-2-Yl] Carbonyl-2- Carbamoyl-4-(6-Chloronaphth-2-Ylsulphonyl)Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca261

b:49.8
occ:1.00
 OD1 A:ASP70 2.2 37.5 1.0
O A:GLN75 2.3 59.1 1.0
O A:ASN72 2.3 43.3 1.0
OE2 A:GLU80 2.4 43.3 1.0
O A:HOH710 2.5 41.5 1.0
O A:HOH808 2.7 57.4 1.0
CG A:ASP70 3.4 36.6 1.0
C A:ASN72 3.4 41.7 1.0
CD A:GLU80 3.4 43.2 1.0
C A:GLN75 3.5 60.3 1.0
OD2 A:ASP70 3.7 37.8 1.0
CG A:GLU80 3.7 39.7 1.0
N A:ASN72 3.9 36.8 1.0
N A:GLU77 4.2 61.8 1.0
CA A:ASN72 4.2 38.3 1.0
N A:THR73 4.3 43.6 1.0
CA A:THR73 4.3 48.0 1.0
CA A:GLU76 4.4 61.7 1.0
N A:GLU76 4.4 61.1 1.0
N A:ARG71 4.4 34.2 1.0
N A:GLN75 4.4 57.8 1.0
CB A:ASN72 4.5 37.1 1.0
CA A:GLN75 4.5 58.8 1.0
CB A:ASP70 4.6 33.7 1.0
OE1 A:GLU80 4.6 42.3 1.0
CA A:ASP70 4.7 33.8 1.0
C A:GLU76 4.8 62.6 1.0
C A:THR73 4.8 50.9 1.0
CB A:GLU77 4.8 61.4 1.0

Calcium binding site 2 out of 2 in 1v3x

Go back to Calcium Binding Sites List in 1v3x
Calcium binding site 2 out of 2 in the Factor Xa in Complex with the Inhibitor 1-[6-Methyl-4,5,6,7- Tetrahydrothiazolo(5,4-C)Pyridin-2-Yl] Carbonyl-2- Carbamoyl-4-(6-Chloronaphth-2-Ylsulphonyl)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 1-[6-Methyl-4,5,6,7- Tetrahydrothiazolo(5,4-C)Pyridin-2-Yl] Carbonyl-2- Carbamoyl-4-(6-Chloronaphth-2-Ylsulphonyl)Piperazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca262

b:58.6
occ:1.00
 O A:LYS224 2.3 40.9 1.0
O A:ARG222 2.3 43.9 1.0
O A:TYR185 2.4 36.8 1.0
O A:ASP185A 2.6 41.3 1.0
O A:HOH732 2.6 36.8 1.0
O A:HOH716 2.9 32.7 1.0
C A:ASP185A 3.4 41.8 1.0
C A:LYS224 3.4 40.7 1.0
C A:ARG222 3.4 43.0 1.0
C A:TYR185 3.5 37.2 1.0
N A:LYS224 3.5 41.3 1.0
CA A:ASP185A 3.9 41.4 1.0
CA A:LYS224 4.0 39.8 1.0
C A:ALA221 4.0 42.0 1.0
N A:GLY223A 4.1 42.9 1.0
O A:ALA221 4.1 43.2 1.0
N A:ARG222 4.1 41.7 1.0
N A:ASP185A 4.2 39.8 1.0
CA A:LYS223 4.2 42.5 1.0
N A:LYS223 4.2 41.7 1.0
N A:THR185B 4.3 41.5 1.0
O A:HOH723 4.3 34.6 1.0
C A:LYS223 4.3 42.3 1.0
CA A:ARG222 4.4 42.4 1.0
CA A:ALA221 4.4 41.9 1.0
N A:TYR225 4.6 40.8 1.0
C A:GLY223A 4.6 42.9 1.0
CB A:LYS224 4.6 39.5 1.0
CA A:THR185B 4.6 41.7 1.0
CA A:TYR185 4.6 37.0 1.0
O A:LYS186 4.7 45.1 1.0
N A:TYR185 4.8 35.9 1.0
CA A:GLY223A 4.8 43.5 1.0
CA A:TYR225 4.9 39.1 1.0
C A:THR185B 4.9 41.3 1.0
CB A:TYR185 5.0 36.1 1.0

Reference:

N.Haginoya, S.Kobayashi, S.Komoriya, T.Yoshino, M.Suzuki, T.Shimada, K.Watanabe, Y.Hirokawa, T.Furugori, T.Nagahara. Synthesis and Conformational Analysis of A Non-Amidine Factor Xa Inhibitor That Incorporates 5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridine As S4 Binding Element J.Med.Chem. V. 47 5167 2004.
ISSN: ISSN 0022-2623
PubMed: 15456260
DOI: 10.1021/JM049884D
Page generated: Tue Jul 8 02:52:39 2025

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