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Calcium in PDB 7g4a: Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl 2-(1H-Benzotriazole-5-Carbonyl)-2,7- Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1C(Cc(CC1S(=O)(=O) C)Coc(=O)N1CCC2(CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)Cl with IC50=0.332347 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl 2-(1H-Benzotriazole-5-Carbonyl)-2,7- Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1C(Cc(CC1S(=O)(=O) C)Coc(=O)N1CCC2(CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)Cl with IC50=0.332347 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl 2-(1H-Benzotriazole-5-Carbonyl)-2,7- Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1C(Cc(CC1S(=O)(=O) C)Coc(=O)N1CCC2(CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)Cl with IC50=0.332347 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl 2-(1H-Benzotriazole-5-Carbonyl)-2,7- Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1C(Cc(CC1S(=O)(=O) C)Coc(=O)N1CCC2(CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)Cl with IC50=0.332347 Microm, PDB code: 7g4a was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.58 / 2.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.806, 93.169, 119.884, 90, 90, 90
R / Rfree (%) 21.2 / 29.4

Other elements in 7g4a:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl 2-(1H-Benzotriazole-5-Carbonyl)-2,7- Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1C(Cc(CC1S(=O)(=O) C)Coc(=O)N1CCC2(CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)Cl with IC50=0.332347 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl 2-(1H-Benzotriazole-5-Carbonyl)-2,7- Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1C(Cc(CC1S(=O)(=O) C)Coc(=O)N1CCC2(CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)Cl with IC50=0.332347 Microm (pdb code 7g4a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl 2-(1H-Benzotriazole-5-Carbonyl)-2,7- Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1C(Cc(CC1S(=O)(=O) C)Coc(=O)N1CCC2(CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)Cl with IC50=0.332347 Microm, PDB code: 7g4a:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g4a

Go back to Calcium Binding Sites List in 7g4a
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl 2-(1H-Benzotriazole-5-Carbonyl)-2,7- Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1C(Cc(CC1S(=O)(=O) C)Coc(=O)N1CCC2(CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)Cl with IC50=0.332347 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl 2-(1H-Benzotriazole-5-Carbonyl)-2,7- Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1C(Cc(CC1S(=O)(=O) C)Coc(=O)N1CCC2(CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)Cl with IC50=0.332347 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:28.8
occ:1.00
 OD1 A:ASP171 2.1 40.1 1.0
OG1 A:THR209 2.1 44.1 1.0
OD2 A:ASP358 2.2 27.9 1.0
NE2 A:HIS359 2.2 28.1 1.0
OD2 A:ASP171 2.4 42.6 1.0
CG2 A:THR209 2.5 29.3 1.0
CG A:ASP171 2.5 35.3 1.0
CB A:THR209 2.6 46.5 1.0
CD2 A:HIS359 3.0 27.4 1.0
CA A:THR209 3.1 45.7 1.0
CG A:ASP358 3.1 37.0 1.0
CE1 A:HIS359 3.2 44.5 1.0
OD1 A:ASP358 3.4 35.4 1.0
C29 A:YOQ901 3.7 47.6 1.0
N A:THR209 3.7 44.3 1.0
CB A:ASP171 4.0 33.1 1.0
CE1 A:HIS474 4.1 56.7 1.0
OD1 A:ASP311 4.1 29.9 1.0
CG A:HIS359 4.2 27.1 1.0
ND1 A:HIS359 4.2 46.7 1.0
C32 A:YOQ901 4.2 45.6 1.0
C A:THR209 4.4 47.5 1.0
NE2 A:HIS474 4.4 29.5 1.0
C28 A:YOQ901 4.4 51.2 1.0
N33 A:YOQ901 4.4 41.8 1.0
CB A:ASP358 4.5 27.0 1.0
CG A:ASP311 4.5 56.2 1.0
ZN A:ZN904 4.5 30.5 1.0
N A:GLY172 4.6 38.7 1.0
C A:LYS208 4.6 27.7 1.0
CA A:ASP171 4.7 37.2 1.0
O A:THR209 4.8 47.0 1.0
OD2 A:ASP311 4.9 64.0 1.0
ND1 A:HIS474 4.9 28.5 1.0
C A:ASP171 4.9 41.6 1.0

Calcium binding site 2 out of 2 in 7g4a

Go back to Calcium Binding Sites List in 7g4a
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl 2-(1H-Benzotriazole-5-Carbonyl)-2,7- Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1C(Cc(CC1S(=O)(=O) C)Coc(=O)N1CCC2(CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)Cl with IC50=0.332347 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl 2-(1H-Benzotriazole-5-Carbonyl)-2,7- Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1C(Cc(CC1S(=O)(=O) C)Coc(=O)N1CCC2(CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2)Cl with IC50=0.332347 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:39.0
occ:1.00
 O A:LEU745 2.0 46.0 1.0
OD1 A:ASP747 2.1 44.6 1.0
OD1 A:ASN741 2.2 36.0 1.0
OD1 A:ASP743 2.3 54.3 1.0
OD1 A:ASP739 2.4 42.3 1.0
CG A:ASN741 2.9 39.4 1.0
ND2 A:ASN741 3.0 40.0 1.0
CG A:ASP743 3.1 50.9 1.0
C A:LEU745 3.2 40.6 1.0
CG A:ASP747 3.4 52.5 1.0
OD2 A:ASP743 3.4 51.3 1.0
CG A:ASP739 3.5 36.1 1.0
N A:ASP747 3.8 40.3 1.0
C A:ARG746 3.8 26.6 1.0
N A:LEU745 3.9 25.2 1.0
CA A:LEU745 4.0 34.4 1.0
O A:ARG746 4.0 38.1 1.0
CA A:ASP747 4.1 43.0 1.0
CA A:ASP739 4.1 34.4 1.0
N A:ARG746 4.1 25.6 1.0
OD2 A:ASP747 4.2 61.5 1.0
CB A:ASP739 4.2 33.0 1.0
CB A:ASP747 4.3 46.1 1.0
CB A:LEU745 4.3 40.8 1.0
CA A:ARG746 4.4 25.9 1.0
CB A:ASN741 4.4 29.1 1.0
CB A:ASP743 4.5 44.0 1.0
O A:PHE738 4.5 26.5 1.0
OD2 A:ASP739 4.5 25.7 1.0
N A:ASP743 4.5 31.8 1.0
N A:ASN741 4.6 28.6 1.0
C A:ASP739 4.7 37.3 1.0
N A:GLY744 4.8 25.4 1.0
CA A:ASP743 4.9 32.0 1.0
CA A:ASN741 4.9 30.6 1.0
N A:TYR740 4.9 28.0 1.0

Reference:

D.Hunziker, S.C.Joachim, C.Ullmer, M.G.Rudolph. Crystal Structure of A Rat Autotaxin Complex To Be Published.
Page generated: Sat Feb 8 15:43:02 2025

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