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Calcium in PDB 7g40: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[1-(2,2,2-Trifluoroethoxy)Isoquinoline-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)C1NC(C2C(C1)CCCC2)Occ(F)(F)F with IC50=0.0187536 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[1-(2,2,2-Trifluoroethoxy)Isoquinoline-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)C1NC(C2C(C1)CCCC2)Occ(F)(F)F with IC50=0.0187536 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[1-(2,2,2-Trifluoroethoxy)Isoquinoline-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)C1NC(C2C(C1)CCCC2)Occ(F)(F)F with IC50=0.0187536 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,2S,6R,7S)-9-[1-(2,2,2-Trifluoroethoxy)Isoquinoline-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)C1NC(C2C(C1)CCCC2)Occ(F)(F)F with IC50=0.0187536 Microm, PDB code: 7g40 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) 48.66 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.761, 91.458, 119.565, 90, 90, 90
R / Rfree (%) 18.7 / 22.8

Other elements in 7g40:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[1-(2,2,2-Trifluoroethoxy)Isoquinoline-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)C1NC(C2C(C1)CCCC2)Occ(F)(F)F with IC50=0.0187536 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Sodium (Na) 1 atom
Fluorine (F) 6 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,2S,6R,7S)-9-[1-(2,2,2-Trifluoroethoxy)Isoquinoline-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)C1NC(C2C(C1)CCCC2)Occ(F)(F)F with IC50=0.0187536 Microm (pdb code 7g40). 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,2S,6R,7S)-9-[1-(2,2,2-Trifluoroethoxy)Isoquinoline-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)C1NC(C2C(C1)CCCC2)Occ(F)(F)F with IC50=0.0187536 Microm, PDB code: 7g40:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g40

Go back to Calcium Binding Sites List in 7g40
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[1-(2,2,2-Trifluoroethoxy)Isoquinoline-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)C1NC(C2C(C1)CCCC2)Occ(F)(F)F with IC50=0.0187536 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,2S,6R,7S)-9-[1-(2,2,2-Trifluoroethoxy)Isoquinoline-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)C1NC(C2C(C1)CCCC2)Occ(F)(F)F with IC50=0.0187536 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:31.3
occ:1.00
 OXT A:ACT902 2.1 36.7 1.0
O A:ASP672 2.2 31.4 1.0
O A:MET675 2.2 27.3 1.0
O A:TYR669 2.3 35.9 1.0
O A:HOH1148 2.4 30.5 1.0
O A:HOH1358 2.5 44.0 1.0
C A:ACT902 3.3 37.6 1.0
C A:MET675 3.4 29.6 1.0
C A:ASP672 3.4 33.3 1.0
C A:TYR669 3.4 34.9 1.0
O A:ACT902 4.0 43.4 1.0
N A:MET675 4.1 31.6 1.0
CA A:TYR669 4.2 30.8 1.0
N A:SER676 4.3 27.4 1.0
O A:LYS670 4.3 41.7 1.0
N A:LYS673 4.3 35.4 1.0
CA A:LYS673 4.3 36.0 1.0
CA A:MET675 4.3 30.0 1.0
CA A:SER676 4.3 28.3 1.0
CH3 A:ACT902 4.4 30.1 1.0
C A:LYS673 4.4 37.0 1.0
N A:LYS670 4.4 35.4 1.0
CA A:ASP672 4.4 33.9 1.0
O A:LYS673 4.5 34.6 1.0
CB A:TYR669 4.6 30.3 1.0
C A:LYS670 4.6 37.7 1.0
N A:ASP672 4.6 35.5 1.0
CB A:ASP672 4.6 33.0 1.0
CA A:LYS670 4.6 39.3 1.0
N A:GLN674 4.9 36.6 1.0
C A:GLN674 4.9 36.8 1.0
CB A:SER676 5.0 29.5 1.0

Calcium binding site 2 out of 2 in 7g40

Go back to Calcium Binding Sites List in 7g40
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[1-(2,2,2-Trifluoroethoxy)Isoquinoline-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)C1NC(C2C(C1)CCCC2)Occ(F)(F)F with IC50=0.0187536 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,2S,6R,7S)-9-[1-(2,2,2-Trifluoroethoxy)Isoquinoline-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)C1NC(C2C(C1)CCCC2)Occ(F)(F)F with IC50=0.0187536 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:21.9
occ:1.00
 OD1 A:ASP739 2.2 18.8 1.0
OD1 A:ASP747 2.2 21.5 1.0
OD1 A:ASN741 2.3 24.5 1.0
O A:LEU745 2.3 19.4 1.0
O A:HOH1354 2.3 24.1 1.0
OD1 A:ASP743 2.4 25.8 1.0
CG A:ASP743 3.3 25.4 1.0
CG A:ASP739 3.4 21.6 1.0
CG A:ASN741 3.4 27.0 1.0
C A:LEU745 3.4 21.2 1.0
CG A:ASP747 3.5 22.9 1.0
OD2 A:ASP743 3.7 27.0 1.0
CA A:ASP739 3.9 20.2 1.0
ND2 A:ASN741 3.9 27.3 1.0
N A:ASP747 4.0 24.0 1.0
C A:ARG746 4.1 24.8 1.0
N A:LEU745 4.1 19.9 1.0
CB A:ASP739 4.1 20.8 1.0
CA A:ASP747 4.2 23.3 1.0
CA A:LEU745 4.2 21.2 1.0
O A:ARG746 4.3 23.3 1.0
N A:ASP743 4.3 22.5 1.0
OD2 A:ASP739 4.3 20.4 1.0
OD2 A:ASP747 4.3 24.7 1.0
O A:PHE738 4.4 20.3 1.0
C A:ASP739 4.4 21.6 1.0
CB A:ASP747 4.4 22.6 1.0
N A:ARG746 4.5 21.3 1.0
CB A:LEU745 4.5 22.8 1.0
N A:ASN741 4.5 23.8 1.0
CB A:ASP743 4.5 23.2 1.0
OE1 A:GLU751 4.6 30.5 0.3
N A:TYR740 4.7 22.6 1.0
CB A:ASN741 4.7 24.3 1.0
CA A:ARG746 4.7 22.4 1.0
N A:TYR742 4.8 22.4 1.0
CA A:ASP743 4.8 23.5 1.0
N A:GLY744 4.8 23.1 1.0
C A:ASN741 4.9 24.1 1.0
OE2 A:GLU751 4.9 34.4 0.7
CA A:ASN741 4.9 23.4 1.0
C A:ASP743 5.0 22.4 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 15:43:01 2025

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