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Zinc in PDB 7g63: Crystal Structure of Rat Autotaxin in Complex with [4-Cyano-2-(2,2- Dimethylpropanoylamino)Phenyl]Methyl (3AS,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1C(Cc(CC1)C#N)Nc(=O)C(C)(C)C with IC50=0.0139432 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4-Cyano-2-(2,2- Dimethylpropanoylamino)Phenyl]Methyl (3AS,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1C(Cc(CC1)C#N)Nc(=O)C(C)(C)C with IC50=0.0139432 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4-Cyano-2-(2,2- Dimethylpropanoylamino)Phenyl]Methyl (3AS,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1C(Cc(CC1)C#N)Nc(=O)C(C)(C)C with IC50=0.0139432 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [4-Cyano-2-(2,2- Dimethylpropanoylamino)Phenyl]Methyl (3AS,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1C(Cc(CC1)C#N)Nc(=O)C(C)(C)C with IC50=0.0139432 Microm, PDB code: 7g63 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) 46.38 / 2.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.949, 92.763, 119.159, 90, 90, 90
R / Rfree (%) 20.5 / 25.2

Other elements in 7g63:

The structure of Crystal Structure of Rat Autotaxin in Complex with [4-Cyano-2-(2,2- Dimethylpropanoylamino)Phenyl]Methyl (3AS,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1C(Cc(CC1)C#N)Nc(=O)C(C)(C)C with IC50=0.0139432 Microm also contains other interesting chemical elements:

Potassium (K) 1 atom
Calcium (Ca) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin in Complex with [4-Cyano-2-(2,2- Dimethylpropanoylamino)Phenyl]Methyl (3AS,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1C(Cc(CC1)C#N)Nc(=O)C(C)(C)C with IC50=0.0139432 Microm (pdb code 7g63). 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 [4-Cyano-2-(2,2- Dimethylpropanoylamino)Phenyl]Methyl (3AS,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1C(Cc(CC1)C#N)Nc(=O)C(C)(C)C with IC50=0.0139432 Microm, PDB code: 7g63:

Zinc binding site 1 out of 1 in 7g63

Go back to Zinc Binding Sites List in 7g63
Zinc binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with [4-Cyano-2-(2,2- Dimethylpropanoylamino)Phenyl]Methyl (3AS,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1C(Cc(CC1)C#N)Nc(=O)C(C)(C)C with IC50=0.0139432 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 [4-Cyano-2-(2,2- Dimethylpropanoylamino)Phenyl]Methyl (3AS,6AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) OCC1C(Cc(CC1)C#N)Nc(=O)C(C)(C)C with IC50=0.0139432 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn905

b:37.9
occ:1.00
 N20 A:Y3B901 1.7 42.9 1.0
OD2 A:ASP311 1.9 28.8 1.0
NE2 A:HIS474 2.1 35.7 1.0
NE2 A:HIS315 2.1 39.5 1.0
OD1 A:ASP311 2.5 35.3 1.0
CG A:ASP311 2.6 34.4 1.0
N21 A:Y3B901 2.6 48.9 1.0
N19 A:Y3B901 2.8 44.1 1.0
CD2 A:HIS474 2.9 34.5 1.0
CD2 A:HIS315 3.0 38.0 1.0
CE1 A:HIS474 3.1 34.0 1.0
CE1 A:HIS315 3.2 38.5 1.0
C17 A:Y3B901 3.9 44.3 1.0
C18 A:Y3B901 3.9 43.2 1.0
CE1 A:HIS359 4.1 34.1 1.0
CB A:ASP311 4.1 32.9 1.0
CG A:HIS474 4.1 34.9 1.0
OG1 A:THR209 4.1 36.2 1.0
ND1 A:HIS474 4.2 36.0 1.0
CG A:HIS315 4.2 40.0 1.0
ND1 A:HIS315 4.3 41.1 1.0
OD2 A:ASP171 4.4 42.0 1.0
NE2 A:HIS359 4.5 34.6 1.0
CE A:MET361 4.6 34.7 1.0
OD1 A:ASP171 4.7 38.4 1.0
O A:ASP311 4.8 42.0 1.0
CG A:ASP171 4.9 37.5 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: Sun Feb 9 00:33:09 2025

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