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Calcium in PDB 7g5u: Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm, PDB code: 7g5u 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) 45.86 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.092, 91.713, 119.99, 90, 90, 90
R / Rfree (%) 20.1 / 24.1

Other elements in 7g5u:

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm (pdb code 7g5u). 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 [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm, PDB code: 7g5u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g5u

Go back to Calcium Binding Sites List in 7g5u
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 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 [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:56.1
occ:1.00
 OG1 A:THR209 1.9 32.5 1.0
OD1 A:ASP171 2.1 29.6 1.0
NE2 A:HIS359 2.2 26.3 1.0
OD2 A:ASP358 2.4 28.9 1.0
CG A:ASP171 2.8 28.3 1.0
CB A:THR209 2.9 29.8 1.0
OD2 A:ASP171 2.9 31.7 1.0
CE1 A:HIS359 3.0 24.0 1.0
CG A:ASP358 3.2 26.3 1.0
CA A:THR209 3.2 27.7 1.0
CD2 A:HIS359 3.3 25.2 1.0
CG2 A:THR209 3.3 29.2 1.0
OD1 A:ASP358 3.3 23.5 1.0
N A:THR209 3.9 28.9 1.0
C15 A:YG2901 4.0 37.5 1.0
OD2 A:ASP311 4.1 30.2 1.0
ND1 A:HIS359 4.1 24.2 1.0
CE1 A:HIS474 4.2 24.4 1.0
CB A:ASP171 4.2 26.7 1.0
CG A:HIS359 4.3 26.4 1.0
NE2 A:HIS474 4.3 24.4 1.0
N19 A:YG2901 4.4 33.8 1.0
C18 A:YG2901 4.4 38.8 1.0
ZN A:ZN906 4.4 29.6 1.0
N A:GLY172 4.4 26.6 1.0
CG A:ASP311 4.4 30.1 1.0
C A:THR209 4.5 27.5 1.0
CB A:ASP358 4.6 25.2 1.0
CA A:ASP171 4.6 26.6 1.0
C A:LYS208 4.7 29.2 1.0
CB A:ASP311 4.8 28.5 1.0
O A:THR209 4.9 26.4 1.0
C A:ASP171 4.9 26.9 1.0
OD1 A:ASP311 4.9 35.2 1.0
C14 A:YG2901 4.9 42.5 1.0
ND1 A:HIS474 4.9 23.1 1.0

Calcium binding site 2 out of 2 in 7g5u

Go back to Calcium Binding Sites List in 7g5u
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 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 [(3AS,6AS)-5-[4-(2, 2,2-Trifluoroethoxy)Quinoline-2-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1NC2C(C(C1)Occ(F)(F)F) CCCC2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0117937 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:24.3
occ:1.00
 OD1 A:ASP747 2.2 22.0 1.0
OD1 A:ASP743 2.3 24.9 1.0
OD1 A:ASN741 2.3 27.8 1.0
O A:HOH1287 2.3 29.8 1.0
O A:LEU745 2.3 23.1 1.0
OD1 A:ASP739 2.3 21.0 1.0
CG A:ASP743 3.3 24.2 1.0
CG A:ASN741 3.3 27.0 1.0
CG A:ASP747 3.5 22.3 1.0
C A:LEU745 3.5 24.3 1.0
CG A:ASP739 3.5 22.1 1.0
OD2 A:ASP743 3.7 24.8 1.0
ND2 A:ASN741 3.8 25.0 1.0
N A:ASP747 3.9 22.8 1.0
CA A:ASP739 3.9 22.6 1.0
C A:ARG746 4.1 24.3 1.0
N A:LEU745 4.1 23.1 1.0
CA A:ASP747 4.1 23.5 1.0
CB A:ASP739 4.2 22.2 1.0
O A:ARG746 4.2 23.4 1.0
CA A:LEU745 4.2 23.7 1.0
OD2 A:ASP747 4.3 22.3 1.0
N A:ASP743 4.3 24.0 1.0
CB A:ASP747 4.4 22.9 1.0
O A:PHE738 4.4 21.0 1.0
C A:ASP739 4.4 24.7 1.0
N A:ASN741 4.5 24.1 1.0
OD2 A:ASP739 4.5 20.5 1.0
CB A:LEU745 4.5 25.2 1.0
CB A:ASP743 4.5 23.5 1.0
N A:ARG746 4.5 23.2 1.0
CB A:ASN741 4.6 24.7 1.0
OE2 A:GLU751 4.7 38.2 1.0
N A:TYR742 4.7 25.5 1.0
N A:TYR740 4.7 24.0 1.0
CA A:ARG746 4.8 24.0 1.0
CA A:ASP743 4.8 24.0 1.0
C A:ASN741 4.8 25.4 1.0
CA A:ASN741 4.9 24.4 1.0
N A:GLY744 4.9 24.8 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 22:30:40 2025

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