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Calcium in PDB 7g4c: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm, PDB code: 7g4c 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) 45.84 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.835, 91.673, 118.797, 90, 90, 90
R / Rfree (%) 17.6 / 20.9

Other elements in 7g4c:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm also contains other interesting chemical elements:

Sodium (Na) 3 atoms
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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm (pdb code 7g4c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm, PDB code: 7g4c:

Calcium binding site 1 out of 1 in 7g4c

Go back to Calcium Binding Sites List in 7g4c
Calcium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(1-Ethyl-4-Propan-2-Yloxyindole-6-Carbonyl)- 4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC2C(C(C1)Oc(C)C)C=CN2CC with IC50=0.0412147 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:12.0
occ:1.00
 O A:LEU745 2.3 13.1 1.0
OD1 A:ASN741 2.3 14.3 1.0
OD1 A:ASP739 2.3 11.9 1.0
OD1 A:ASP747 2.3 13.9 1.0
OD1 A:ASP743 2.3 14.0 1.0
O A:HOH1437 2.3 18.0 1.0
CG A:ASP743 3.3 14.7 1.0
CG A:ASN741 3.3 15.9 1.0
CG A:ASP739 3.5 11.4 1.0
C A:LEU745 3.5 10.8 1.0
CG A:ASP747 3.6 14.1 1.0
OD2 A:ASP743 3.7 15.9 1.0
ND2 A:ASN741 3.7 20.2 1.0
N A:ASP747 3.9 11.7 1.0
CA A:ASP739 4.0 9.6 1.0
C A:ARG746 4.0 11.5 1.0
N A:LEU745 4.1 10.6 1.0
CA A:ASP747 4.1 11.3 1.0
O A:ARG746 4.2 12.6 1.0
CB A:ASP739 4.2 11.9 1.0
CA A:LEU745 4.2 10.9 1.0
N A:ASP743 4.3 11.4 1.0
OD2 A:ASP739 4.4 11.3 1.0
OD2 A:ASP747 4.4 16.6 1.0
O A:PHE738 4.4 13.2 1.0
CB A:ASP747 4.4 12.3 1.0
N A:ASN741 4.5 12.3 1.0
N A:ARG746 4.5 10.5 1.0
C A:ASP739 4.5 10.9 1.0
CB A:LEU745 4.5 13.2 1.0
CB A:ASP743 4.6 13.0 1.0
OE2 A:GLU751 4.6 25.8 1.0
CB A:ASN741 4.6 13.6 1.0
N A:TYR740 4.7 11.0 1.0
CA A:ARG746 4.7 10.1 1.0
O A:HOH1387 4.7 28.1 1.0
N A:TYR742 4.8 13.2 1.0
CA A:ASP743 4.8 12.8 1.0
CA A:ASN741 4.9 12.1 1.0
N A:GLY744 4.9 12.2 1.0
C A:ASN741 4.9 13.9 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: Wed Jul 9 22:25:19 2025

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