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Calcium in PDB 7g64: Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm, PDB code: 7g64 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) 45.88 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.38, 91.754, 121.021, 90, 90, 90
R / Rfree (%) 19.5 / 24.9

Other elements in 7g64:

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Potassium (K) 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 [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm (pdb code 7g64). 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-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm, PDB code: 7g64:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g64

Go back to Calcium Binding Sites List in 7g64
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 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-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:62.2
occ:1.00
 OD1 A:ASP171 2.2 31.6 1.0
NE2 A:HIS359 2.2 25.7 1.0
OG1 A:THR209 2.3 37.1 1.0
OD2 A:ASP358 2.7 29.7 1.0
CB A:THR209 2.9 32.6 1.0
CG2 A:THR209 2.9 32.3 1.0
CG A:ASP171 2.9 30.1 1.0
OD2 A:ASP171 3.0 35.8 1.0
CE1 A:HIS359 3.1 23.9 1.0
CA A:THR209 3.1 28.8 1.0
CD2 A:HIS359 3.2 24.3 1.0
CG A:ASP358 3.5 29.6 1.0
N A:THR209 3.7 28.2 1.0
OD1 A:ASP358 3.7 26.3 1.0
C15 A:YDV904 4.0 35.5 1.0
CE1 A:HIS474 4.0 25.1 1.0
OD2 A:ASP311 4.1 27.2 1.0
N19 A:YDV904 4.1 32.4 1.0
C18 A:YDV904 4.1 36.9 1.0
ND1 A:HIS359 4.2 21.6 1.0
ZN A:ZN905 4.2 27.0 1.0
NE2 A:HIS474 4.3 23.9 1.0
CG A:HIS359 4.3 23.6 1.0
CB A:ASP171 4.3 27.8 1.0
C A:THR209 4.4 27.0 1.0
CG A:ASP311 4.4 28.2 1.0
C A:LYS208 4.5 30.0 1.0
N A:GLY172 4.6 24.4 1.0
CB A:ASP358 4.7 26.5 1.0
CA A:ASP171 4.7 23.6 1.0
C14 A:YDV904 4.8 42.2 1.0
OD1 A:ASP311 4.8 28.8 1.0
O A:THR209 4.8 24.7 1.0
ND1 A:HIS474 4.9 22.8 1.0
N20 A:YDV904 4.9 39.5 1.0

Calcium binding site 2 out of 2 in 7g64

Go back to Calcium Binding Sites List in 7g64
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 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-[5- Cyclopropyl-6-(2,2,2-Trifluoroethoxy)Pyridine-3-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)C1CC(C(NC1) Occ(F)(F)F)C1CC1)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.0111778 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:27.5
occ:1.00
 O A:HOH1285 2.3 39.2 1.0
OD1 A:ASP739 2.3 26.0 1.0
OD1 A:ASP747 2.3 25.6 1.0
O A:LEU745 2.3 23.4 1.0
OD1 A:ASP743 2.3 31.8 1.0
OD1 A:ASN741 2.4 29.7 1.0
CG A:ASP743 3.3 31.9 1.0
CG A:ASN741 3.4 33.6 1.0
CG A:ASP739 3.5 25.2 1.0
C A:LEU745 3.5 26.2 1.0
CG A:ASP747 3.5 27.2 1.0
ND2 A:ASN741 3.7 30.1 1.0
OD2 A:ASP743 3.8 36.3 1.0
CA A:ASP739 4.0 23.1 1.0
N A:LEU745 4.0 22.2 1.0
C A:ARG746 4.0 24.9 1.0
N A:ASP747 4.0 23.6 1.0
O A:ARG746 4.1 24.5 1.0
CB A:ASP739 4.2 22.4 1.0
CA A:ASP747 4.2 23.9 1.0
CA A:LEU745 4.2 23.2 1.0
N A:ASP743 4.3 25.9 1.0
OD2 A:ASP747 4.4 28.5 1.0
OD2 A:ASP739 4.4 24.0 1.0
O A:PHE738 4.4 23.2 1.0
CB A:ASP747 4.5 23.2 1.0
CB A:LEU745 4.5 28.2 1.0
N A:ASN741 4.5 26.9 1.0
N A:ARG746 4.5 22.8 1.0
C A:ASP739 4.5 26.8 1.0
CB A:ASP743 4.6 26.1 1.0
CB A:ASN741 4.7 27.5 1.0
CA A:ARG746 4.7 24.0 1.0
OE2 A:GLU751 4.8 51.3 1.0
N A:TYR742 4.8 28.4 1.0
N A:GLY744 4.8 24.7 1.0
N A:TYR740 4.8 24.1 1.0
CA A:ASP743 4.8 26.3 1.0
C A:ASN741 4.9 28.6 1.0
CA A:ASN741 4.9 28.1 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 15:55:17 2025

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