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Chlorine 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:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 1 in 2ei8

Go back to Chlorine Binding Sites List in 2ei8
Chlorine binding site 1 out of 1 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 Chlorine with other atoms in the Cl 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:Cl700

b:34.5
occ:1.00
 CL1 A:DT8700 0.0 34.5 1.0
C2 A:DT8700 1.8 37.2 1.0
C3 A:DT8700 2.7 36.7 1.0
C1 A:DT8700 2.8 36.0 1.0
CZ A:TYR228 3.3 29.0 1.0
O A:ILE227 3.5 26.2 1.0
CE2 A:TYR228 3.5 27.7 1.0
N A:ILE227 3.6 29.0 1.0
OH A:TYR228 3.6 28.3 1.0
CE1 A:TYR228 3.6 28.7 1.0
CA A:GLY226 3.6 32.1 1.0
CG1 A:VAL213 3.8 24.4 1.0
C A:GLY226 3.8 30.0 1.0
O A:TRP215 3.9 30.3 1.0
CB A:ALA190 3.9 27.6 1.0
C A:ILE227 3.9 27.5 1.0
C4 A:DT8700 4.0 36.4 1.0
CD2 A:TYR228 4.0 28.7 1.0
C6 A:DT8700 4.0 36.3 1.0
CD1 A:TYR228 4.1 25.9 1.0
N A:SER214 4.2 27.9 1.0
CG A:TYR228 4.3 28.4 1.0
CA A:ILE227 4.4 27.6 1.0
CA A:VAL213 4.4 26.1 1.0
O A:HOH701 4.4 32.6 1.0
C5 A:DT8700 4.5 36.1 1.0
C A:TRP215 4.5 31.7 1.0
CB A:VAL213 4.6 25.1 1.0
N A:TRP215 4.6 33.1 1.0
O A:GLY226 4.7 31.7 1.0
N A:TYR228 4.7 26.8 1.0
C A:VAL213 4.7 28.5 1.0
CG2 A:VAL213 4.9 24.4 1.0
OD1 A:ASP189 5.0 32.8 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: Thu Jul 10 22:00:18 2025

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