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Zinc 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
Calcium (Ca) 2 atoms
Potassium (K) 1 atom
Fluorine (F) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was 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:

Zinc binding site 1 out of 1 in 7g64

Go back to Zinc Binding Sites List in 7g64
Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn905

b:27.0
occ:1.00
 N19 A:YDV904 1.7 32.4 1.0
OD2 A:ASP311 2.0 27.2 1.0
NE2 A:HIS315 2.1 31.7 1.0
NE2 A:HIS474 2.2 23.9 1.0
N20 A:YDV904 2.5 39.5 1.0
OD1 A:ASP311 2.5 28.8 1.0
CG A:ASP311 2.6 28.2 1.0
C18 A:YDV904 3.0 36.9 1.0
CD2 A:HIS315 3.0 30.9 1.0
CE1 A:HIS315 3.1 32.8 1.0
CD2 A:HIS474 3.1 22.2 1.0
CE1 A:HIS474 3.2 25.1 1.0
N21 A:YDV904 3.7 39.6 1.0
C15 A:YDV904 3.7 35.5 1.0
C17 A:YDV904 4.0 40.2 1.0
CB A:ASP311 4.1 27.3 1.0
CG A:HIS315 4.2 31.7 1.0
ND1 A:HIS315 4.2 31.0 1.0
CE1 A:HIS359 4.2 23.9 1.0
CA A:CA901 4.2 62.2 1.0
ND1 A:HIS474 4.3 22.8 1.0
CG A:HIS474 4.3 23.3 1.0
OG1 A:THR209 4.3 37.1 1.0
NE2 A:HIS359 4.5 25.7 1.0
CE A:MET361 4.6 27.8 1.0
OD1 A:ASP171 4.8 31.6 1.0
O A:ASP311 4.8 26.3 1.0
CA A:ASP311 5.0 27.3 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: Sun Feb 9 00:33:09 2025

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