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Calcium in PDB 2ei7: Factor Xa in Complex with the Inhibitor Trans-N1-[(5-Chloroindol-2- Yl)Carbonyl]-N2-[(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin- 2-Yl)Carbonyl]-1,2-Cyclohexanediamine

Enzymatic activity of Factor Xa in Complex with the Inhibitor Trans-N1-[(5-Chloroindol-2- Yl)Carbonyl]-N2-[(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin- 2-Yl)Carbonyl]-1,2-Cyclohexanediamine

All present enzymatic activity of Factor Xa in Complex with the Inhibitor Trans-N1-[(5-Chloroindol-2- Yl)Carbonyl]-N2-[(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin- 2-Yl)Carbonyl]-1,2-Cyclohexanediamine:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with the Inhibitor Trans-N1-[(5-Chloroindol-2- Yl)Carbonyl]-N2-[(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin- 2-Yl)Carbonyl]-1,2-Cyclohexanediamine, PDB code: 2ei7 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 (°) 56.963, 73.035, 79.849, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 27.3

Other elements in 2ei7:

The structure of Factor Xa in Complex with the Inhibitor Trans-N1-[(5-Chloroindol-2- Yl)Carbonyl]-N2-[(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin- 2-Yl)Carbonyl]-1,2-Cyclohexanediamine 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 Trans-N1-[(5-Chloroindol-2- Yl)Carbonyl]-N2-[(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin- 2-Yl)Carbonyl]-1,2-Cyclohexanediamine (pdb code 2ei7). 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 Trans-N1-[(5-Chloroindol-2- Yl)Carbonyl]-N2-[(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin- 2-Yl)Carbonyl]-1,2-Cyclohexanediamine, PDB code: 2ei7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2ei7

Go back to Calcium Binding Sites List in 2ei7
Calcium binding site 1 out of 2 in the Factor Xa in Complex with the Inhibitor Trans-N1-[(5-Chloroindol-2- Yl)Carbonyl]-N2-[(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin- 2-Yl)Carbonyl]-1,2-Cyclohexanediamine


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 Trans-N1-[(5-Chloroindol-2- Yl)Carbonyl]-N2-[(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin- 2-Yl)Carbonyl]-1,2-Cyclohexanediamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca261

b:51.4
occ:1.00
 O A:HOH751 2.2 56.8 1.0
OD1 A:ASP70 2.3 43.4 1.0
O A:ASN72 2.4 47.9 1.0
O A:HOH717 2.5 41.7 1.0
O A:GLN75 2.5 68.8 1.0
OE2 A:GLU80 2.6 52.6 1.0
CG A:ASP70 3.4 43.7 1.0
C A:GLN75 3.4 68.4 1.0
C A:ASN72 3.5 49.4 1.0
CD A:GLU80 3.6 52.8 1.0
N A:GLU77 4.0 67.5 1.0
OD2 A:ASP70 4.0 44.9 1.0
CG A:GLU80 4.0 50.8 1.0
CA A:GLU76 4.0 68.8 1.0
N A:GLU76 4.0 69.0 1.0
N A:ASN72 4.1 46.0 1.0
CA A:THR73 4.3 54.0 1.0
CA A:ASN72 4.3 47.8 1.0
N A:THR73 4.3 51.0 1.0
N A:GLN75 4.5 65.7 1.0
CB A:ASP70 4.5 41.6 1.0
C A:GLU76 4.5 68.3 1.0
CA A:GLN75 4.5 67.1 1.0
OE1 A:GLU80 4.6 54.6 1.0
N A:ARG71 4.6 42.8 1.0
CA A:ASP70 4.6 41.8 1.0
CB A:ASN72 4.7 48.4 1.0
C A:THR73 4.7 56.3 1.0
CB A:GLU77 4.7 67.2 1.0
CA A:GLU77 5.0 66.9 1.0

Calcium binding site 2 out of 2 in 2ei7

Go back to Calcium Binding Sites List in 2ei7
Calcium binding site 2 out of 2 in the Factor Xa in Complex with the Inhibitor Trans-N1-[(5-Chloroindol-2- Yl)Carbonyl]-N2-[(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin- 2-Yl)Carbonyl]-1,2-Cyclohexanediamine


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 Trans-N1-[(5-Chloroindol-2- Yl)Carbonyl]-N2-[(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin- 2-Yl)Carbonyl]-1,2-Cyclohexanediamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca262

b:0.8
occ:1.00
 O A:LYS224 2.3 49.1 1.0
O A:ARG222 2.3 51.9 1.0
O A:TYR185 2.4 44.5 1.0
O A:HOH757 2.5 69.9 1.0
O A:ASP185A 2.9 54.7 1.0
C A:LYS224 3.4 49.6 1.0
C A:ARG222 3.5 52.1 1.0
C A:ASP185A 3.5 53.1 1.0
C A:TYR185 3.6 46.3 1.0
N A:LYS224 3.7 52.4 1.0
O A:ALA221 3.9 45.7 1.0
C A:ALA221 4.0 44.9 1.0
CA A:LYS224 4.0 51.1 1.0
CA A:ASP185A 4.0 52.7 1.0
N A:ARG222 4.2 47.5 1.0
N A:GLY223A 4.2 53.9 1.0
N A:ASP185A 4.3 49.9 1.0
CA A:LYS223 4.3 54.6 1.0
N A:LYS223 4.3 53.6 1.0
O A:HOH744 4.3 42.2 1.0
N A:THR185B 4.4 53.9 1.0
CA A:ARG222 4.5 49.2 1.0
C A:LYS223 4.5 54.4 1.0
N A:TYR225 4.5 48.5 1.0
O A:LYS186 4.5 54.0 1.0
CA A:ALA221 4.5 43.2 1.0
CB A:LYS224 4.5 51.1 1.0
CA A:TYR185 4.6 44.7 1.0
N A:TYR185 4.7 43.1 1.0
C A:GLY223A 4.8 54.0 1.0
CA A:THR185B 4.8 55.1 1.0
CB A:TYR185 4.9 43.5 1.0
CA A:TYR225 4.9 46.1 1.0

Reference:

T.Nagata, T.Yoshino, N.Haginoya, K.Yoshikawa, Y.Isobe, T.Furugohri, H.Kanno. Cycloalkanediamine Derivatives As Novel Blood Coagulation Factor Xa Inhibitors To Be Published.
Page generated: Fri Jul 12 10:13:15 2024

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