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Calcium in PDB 7g5r: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 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-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm, PDB code: 7g5r 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) 48.89 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.288, 91.722, 120.027, 90, 90, 90
R / Rfree (%) 20 / 25

Other elements in 7g5r:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Fluorine (F) 3 atoms

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-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm (pdb code 7g5r). 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm, PDB code: 7g5r:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g5r

Go back to Calcium Binding Sites List in 7g5r
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 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-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:50.9
occ:1.00
 OD1 A:ASP171 2.0 33.6 1.0
OG1 A:THR209 2.0 36.1 1.0
NE2 A:HIS359 2.2 25.5 1.0
OD2 A:ASP358 2.5 28.6 1.0
CG A:ASP171 2.9 30.6 1.0
CB A:THR209 2.9 32.5 1.0
CE1 A:HIS359 3.0 26.5 1.0
CG2 A:THR209 3.1 35.4 1.0
OD2 A:ASP171 3.2 34.4 1.0
CD2 A:HIS359 3.2 25.1 1.0
CG A:ASP358 3.3 27.4 1.0
CA A:THR209 3.3 30.3 1.0
OD1 A:ASP358 3.5 27.2 1.0
N A:THR209 3.9 30.4 1.0
O A:HOH1005 4.1 40.5 1.0
OD1 A:ASP311 4.1 29.7 1.0
ND1 A:HIS359 4.1 26.1 1.0
CB A:ASP171 4.2 29.4 1.0
CE1 A:HIS474 4.2 22.9 1.0
CG A:HIS359 4.3 25.1 1.0
N A:GLY172 4.3 27.6 1.0
C19 A:YQ9902 4.4 33.7 1.0
CG A:ASP311 4.4 28.9 1.0
NE2 A:HIS474 4.4 23.8 1.0
ZN A:ZN903 4.5 29.1 1.0
CA A:ASP171 4.5 27.9 1.0
CB A:ASP358 4.6 27.1 1.0
C A:THR209 4.6 30.5 1.0
C A:LYS208 4.6 30.2 1.0
N23 A:YQ9902 4.6 31.7 1.0
C22 A:YQ9902 4.7 33.5 1.0
OD2 A:ASP311 4.8 28.4 1.0
C A:ASP171 4.8 27.7 1.0
CB A:ASP311 4.9 28.1 1.0
O A:THR209 4.9 30.3 1.0

Calcium binding site 2 out of 2 in 7g5r

Go back to Calcium Binding Sites List in 7g5r
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-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)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:26.0
occ:1.00
 O A:HOH1263 2.2 28.3 1.0
OD1 A:ASP747 2.2 25.6 1.0
OD1 A:ASP743 2.3 25.9 1.0
O A:LEU745 2.4 24.6 1.0
OD1 A:ASP739 2.4 26.0 1.0
OD1 A:ASN741 2.4 29.0 1.0
CG A:ASP743 3.2 25.1 1.0
CG A:ASN741 3.4 27.6 1.0
CG A:ASP747 3.5 24.4 1.0
C A:LEU745 3.5 25.4 1.0
CG A:ASP739 3.6 25.4 1.0
OD2 A:ASP743 3.6 24.6 1.0
ND2 A:ASN741 3.7 24.7 1.0
N A:ASP747 3.8 26.0 1.0
C A:ARG746 4.0 27.5 1.0
CA A:ASP739 4.0 26.4 1.0
CA A:ASP747 4.0 24.7 1.0
N A:LEU745 4.1 24.2 1.0
O A:ARG746 4.1 26.6 1.0
CA A:LEU745 4.2 24.6 1.0
CB A:ASP739 4.3 24.9 1.0
N A:ASP743 4.3 26.2 1.0
OD2 A:ASP747 4.3 24.0 1.0
CB A:ASP747 4.3 22.6 1.0
O A:PHE738 4.4 23.3 1.0
CB A:ASP743 4.5 23.9 1.0
CB A:LEU745 4.5 24.5 1.0
C A:ASP739 4.5 26.4 1.0
N A:ASN741 4.5 25.2 1.0
N A:ARG746 4.5 26.1 1.0
OD2 A:ASP739 4.5 23.6 1.0
OE2 A:GLU751 4.7 37.5 1.0
CB A:ASN741 4.7 24.8 1.0
N A:TYR740 4.7 25.6 1.0
CA A:ARG746 4.7 26.9 1.0
CA A:ASP743 4.8 26.1 1.0
N A:TYR742 4.8 27.9 1.0
N A:GLY744 4.9 25.8 1.0
CA A:ASN741 4.9 26.1 1.0
C A:ASN741 5.0 27.5 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 15:51:37 2025

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