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Calcium in PDB 2ei8: Factor Xa in Complex with the Inhibitor (1S,2R,4S)-N1-[(5- Chloroindol-2-Yl)Carbonyl]-4-(N,N-Dimethylcarbamoyl)-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 (1S,2R,4S)-N1-[(5- Chloroindol-2-Yl)Carbonyl]-4-(N,N-Dimethylcarbamoyl)-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 (1S,2R,4S)-N1-[(5- Chloroindol-2-Yl)Carbonyl]-4-(N,N-Dimethylcarbamoyl)-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 (1S,2R,4S)-N1-[(5- Chloroindol-2-Yl)Carbonyl]-4-(N,N-Dimethylcarbamoyl)-N2- [(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin-2-Yl) Carbonyl]-1,2-Cyclohexanediamine, PDB code: 2ei8 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 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.217, 72.190, 79.325, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25

Other elements in 2ei8:

The structure of Factor Xa in Complex with the Inhibitor (1S,2R,4S)-N1-[(5- Chloroindol-2-Yl)Carbonyl]-4-(N,N-Dimethylcarbamoyl)-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 (1S,2R,4S)-N1-[(5- Chloroindol-2-Yl)Carbonyl]-4-(N,N-Dimethylcarbamoyl)-N2- [(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin-2-Yl) Carbonyl]-1,2-Cyclohexanediamine (pdb code 2ei8). 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 (1S,2R,4S)-N1-[(5- Chloroindol-2-Yl)Carbonyl]-4-(N,N-Dimethylcarbamoyl)-N2- [(5-Methyl-4,5,6,7-Tetrahydrothiazolo[5,4-C]Pyridin-2-Yl) Carbonyl]-1,2-Cyclohexanediamine, PDB code: 2ei8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2ei8

Go back to Calcium Binding Sites List in 2ei8
Calcium binding site 1 out of 2 in the Factor Xa in Complex with the Inhibitor (1S,2R,4S)-N1-[(5- Chloroindol-2-Yl)Carbonyl]-4-(N,N-Dimethylcarbamoyl)-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 (1S,2R,4S)-N1-[(5- Chloroindol-2-Yl)Carbonyl]-4-(N,N-Dimethylcarbamoyl)-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:62.1
occ:1.00
 O A:ARG222 2.3 39.4 1.0
O A:TYR185 2.3 34.7 1.0
O A:LYS224 2.4 37.5 1.0
O A:HOH722 2.4 33.3 1.0
O A:ASP185A 2.7 39.1 1.0
O A:HOH730 2.8 33.1 1.0
C A:ASP185A 3.4 38.6 1.0
C A:ARG222 3.4 39.9 1.0
C A:TYR185 3.5 35.3 1.0
C A:LYS224 3.5 38.7 1.0
N A:LYS224 3.8 40.4 1.0
CA A:ASP185A 3.9 38.5 1.0
C A:ALA221 3.9 37.1 1.0
O A:ALA221 4.0 37.1 1.0
CA A:LYS224 4.1 39.4 1.0
N A:ARG222 4.1 37.2 1.0
N A:ASP185A 4.1 37.3 1.0
N A:THR185B 4.2 38.3 1.0
N A:LYS223 4.2 39.5 1.0
CA A:LYS223 4.2 40.8 1.0
N A:GLY223A 4.3 39.3 1.0
CA A:ALA221 4.3 35.9 1.0
O A:HOH750 4.4 30.7 1.0
CA A:ARG222 4.4 38.8 1.0
CB A:LYS224 4.5 40.6 1.0
C A:LYS223 4.5 39.6 1.0
CA A:THR185B 4.5 37.9 1.0
O A:LYS186 4.6 38.8 1.0
N A:TYR225 4.6 36.9 1.0
CA A:TYR185 4.7 34.9 1.0
C A:GLY223A 4.8 40.8 1.0
N A:TYR185 4.8 34.0 1.0
CA A:TYR225 4.9 36.3 1.0
C A:THR185B 4.9 37.5 1.0
CB A:TYR185 5.0 34.0 1.0

Calcium binding site 2 out of 2 in 2ei8

Go back to Calcium Binding Sites List in 2ei8
Calcium binding site 2 out of 2 in the Factor Xa in Complex with the Inhibitor (1S,2R,4S)-N1-[(5- Chloroindol-2-Yl)Carbonyl]-4-(N,N-Dimethylcarbamoyl)-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 (1S,2R,4S)-N1-[(5- Chloroindol-2-Yl)Carbonyl]-4-(N,N-Dimethylcarbamoyl)-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:43.3
occ:1.00
 O A:GLN75 2.2 59.4 1.0
OE2 A:GLU80 2.3 42.6 1.0
OD1 A:ASP70 2.3 35.0 1.0
O A:ASN72 2.4 33.3 1.0
O A:HOH715 2.4 36.3 1.0
O A:HOH767 2.8 65.0 1.0
CD A:GLU80 3.4 42.3 1.0
C A:ASN72 3.4 35.0 1.0
C A:GLN75 3.4 58.8 1.0
CG A:ASP70 3.4 34.6 1.0
CG A:GLU80 3.9 40.0 1.0
OD2 A:ASP70 4.0 35.2 1.0
N A:ASN72 4.0 33.3 1.0
N A:GLN75 4.2 55.3 1.0
N A:GLU77 4.2 59.1 1.0
CA A:ASN72 4.2 33.9 1.0
O A:HOH799 4.3 64.0 1.0
N A:THR73 4.3 37.0 1.0
CA A:THR73 4.3 41.3 1.0
CA A:GLU76 4.3 60.2 1.0
N A:GLU76 4.3 59.8 1.0
CA A:GLN75 4.4 57.7 1.0
OE1 A:GLU80 4.4 42.1 1.0
CB A:ASN72 4.5 33.4 1.0
C A:THR73 4.6 44.8 1.0
N A:ARG71 4.6 33.2 1.0
CB A:ASP70 4.6 32.1 1.0
O A:THR73 4.7 47.2 1.0
CA A:ASP70 4.8 31.9 1.0
C A:GLU76 4.8 60.1 1.0
CB A:GLN75 4.9 57.5 1.0
CB A:GLU77 4.9 58.7 1.0

Reference:

T.Nagata, T.Yoshino, N.Haginoya, K.Yoshikawa, M.Nagamochi, S.Kobayashi, S.Komoriya, A.Yokomizo, R.Muto, K.Yamaguchi, K.Osanai, M.Suzuki, H.Kanno. Discovery of N-{(1R,2S,5S)-2-{[(5-Chloroindol-2-Yl) Carbonyl]Amino}-5-[(Dimethylamino) Carbonyl]Cyclohexyl}-5-Methyl-4,5,6,7- Tetrahydrothiazolo[5,4-C]Pyridine-2-Carboxamide Hydrochloride: A Novel, Potent and Orally Active Direct Inhibitor of Factor Xa To Be Published.
Page generated: Tue Jul 8 05:22:00 2025

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