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Calcium in PDB 2ei6: Factor Xa in Complex with the Inhibitor (-)-Cis-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 (-)-Cis-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 (-)-Cis-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 (-)-Cis-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: 2ei6 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 (°) 56.805, 72.971, 79.552, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 26.2

Other elements in 2ei6:

The structure of Factor Xa in Complex with the Inhibitor (-)-Cis-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 (-)-Cis-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 2ei6). 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 (-)-Cis-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: 2ei6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2ei6

Go back to Calcium Binding Sites List in 2ei6
Calcium binding site 1 out of 2 in the Factor Xa in Complex with the Inhibitor (-)-Cis-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 (-)-Cis-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:49.1
occ:1.00
 O A:HOH751 2.2 63.5 1.0
O A:HOH713 2.3 51.1 1.0
OD1 A:ASP70 2.3 43.3 1.0
O A:GLN75 2.4 69.0 1.0
OE2 A:GLU80 2.4 52.4 1.0
O A:ASN72 2.5 44.1 1.0
CD A:GLU80 3.3 51.8 1.0
CG A:ASP70 3.4 42.7 1.0
C A:GLN75 3.4 68.2 1.0
C A:ASN72 3.6 44.9 1.0
CG A:GLU80 3.7 49.8 1.0
OD2 A:ASP70 4.0 44.1 1.0
CA A:GLU76 4.0 68.9 1.0
N A:ASN72 4.1 40.4 1.0
N A:GLU76 4.2 68.9 1.0
CA A:THR73 4.2 51.5 1.0
N A:THR73 4.4 47.5 1.0
N A:GLN75 4.4 65.0 1.0
CA A:ASN72 4.4 43.4 1.0
N A:GLU77 4.4 69.2 1.0
OE1 A:GLU80 4.4 53.6 1.0
CA A:GLN75 4.5 66.6 1.0
CB A:ASP70 4.6 40.4 1.0
N A:ARG71 4.6 40.0 1.0
CA A:ASP70 4.7 39.8 1.0
C A:THR73 4.7 54.4 1.0
C A:GLU76 4.8 69.2 1.0
CB A:ASN72 4.8 42.8 1.0

Calcium binding site 2 out of 2 in 2ei6

Go back to Calcium Binding Sites List in 2ei6
Calcium binding site 2 out of 2 in the Factor Xa in Complex with the Inhibitor (-)-Cis-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 (-)-Cis-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:85.3
occ:1.00
 O A:ARG222 2.3 46.9 1.0
O A:TYR185 2.4 40.2 1.0
O A:LYS224 2.5 45.5 1.0
O A:HOH757 2.8 58.9 1.0
O A:ASP185A 3.2 52.8 1.0
C A:ARG222 3.4 47.3 1.0
C A:TYR185 3.6 43.1 1.0
C A:LYS224 3.6 45.5 1.0
C A:ASP185A 3.7 51.5 1.0
N A:LYS224 3.8 47.7 1.0
C A:ALA221 3.8 44.3 1.0
O A:ALA221 3.9 44.2 1.0
N A:ARG222 4.0 45.5 1.0
CA A:ASP185A 4.1 50.3 1.0
CA A:LYS224 4.2 46.5 1.0
N A:LYS223 4.2 47.9 1.0
N A:GLY223A 4.3 49.0 1.0
CA A:LYS223 4.3 48.7 1.0
CA A:ALA221 4.3 43.6 1.0
N A:ASP185A 4.3 47.5 1.0
O A:HOH745 4.3 43.0 1.0
CA A:ARG222 4.4 46.0 1.0
O A:LYS186 4.4 50.0 1.0
C A:LYS223 4.5 48.8 1.0
N A:THR185B 4.5 51.4 1.0
CB A:LYS224 4.7 46.7 1.0
CA A:TYR185 4.7 42.0 1.0
N A:TYR225 4.7 43.2 1.0
N A:TYR185 4.8 41.3 1.0
C A:GLY223A 4.8 49.5 1.0
CA A:THR185B 4.8 52.3 1.0
O A:HOH742 5.0 52.1 1.0
CB A:TYR185 5.0 41.3 1.0
CA A:GLY223A 5.0 49.3 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. Bioorg.Med.Chem.Lett. V. 17 4683 2007.
ISSN: ISSN 0960-894X
PubMed: 17555959
DOI: 10.1016/J.BMCL.2007.05.068
Page generated: Fri Jul 12 10:13:15 2024

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