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Calcium in PDB 7g4j: Crystal Structure of Rat Autotaxin in Complex with 4-[Rac-(E)-3-Oxo-3- [Rac-(3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]Prop-1-Enyl]Benzonitrile, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)C#N)Cn(C2)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.193037 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[Rac-(E)-3-Oxo-3- [Rac-(3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]Prop-1-Enyl]Benzonitrile, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)C#N)Cn(C2)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.193037 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[Rac-(E)-3-Oxo-3- [Rac-(3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]Prop-1-Enyl]Benzonitrile, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)C#N)Cn(C2)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.193037 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[Rac-(E)-3-Oxo-3- [Rac-(3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]Prop-1-Enyl]Benzonitrile, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)C#N)Cn(C2)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.193037 Microm, PDB code: 7g4j 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) 46.46 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.159, 92.834, 121.104, 90, 90, 90
R / Rfree (%) 20.3 / 26

Other elements in 7g4j:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[Rac-(E)-3-Oxo-3- [Rac-(3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]Prop-1-Enyl]Benzonitrile, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)C#N)Cn(C2)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.193037 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-[Rac-(E)-3-Oxo-3- [Rac-(3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]Prop-1-Enyl]Benzonitrile, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)C#N)Cn(C2)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.193037 Microm (pdb code 7g4j). 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 4-[Rac-(E)-3-Oxo-3- [Rac-(3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]Prop-1-Enyl]Benzonitrile, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)C#N)Cn(C2)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.193037 Microm, PDB code: 7g4j:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g4j

Go back to Calcium Binding Sites List in 7g4j
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[Rac-(E)-3-Oxo-3- [Rac-(3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]Prop-1-Enyl]Benzonitrile, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)C#N)Cn(C2)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.193037 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 4-[Rac-(E)-3-Oxo-3- [Rac-(3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]Prop-1-Enyl]Benzonitrile, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)C#N)Cn(C2)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.193037 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:35.1
occ:1.00
 OG1 A:THR209 2.0 44.6 1.0
OD1 A:ASP171 2.1 40.5 1.0
OD2 A:ASP358 2.2 39.7 1.0
NE2 A:HIS359 2.2 33.7 1.0
CG A:ASP171 2.7 39.9 1.0
OD2 A:ASP171 2.8 38.6 1.0
CB A:THR209 2.9 46.7 1.0
CG A:ASP358 3.1 35.7 1.0
CD2 A:HIS359 3.1 33.6 1.0
CE1 A:HIS359 3.1 36.0 1.0
CG2 A:THR209 3.2 51.5 1.0
OD1 A:ASP358 3.2 37.7 1.0
CA A:THR209 3.2 45.0 1.0
N A:THR209 3.8 45.6 1.0
C17 A:YN2902 4.1 39.8 1.0
ND1 A:HIS359 4.1 35.6 1.0
OD1 A:ASP311 4.1 33.1 1.0
CG A:HIS359 4.1 35.3 1.0
CB A:ASP171 4.2 36.8 1.0
N A:GLY172 4.4 32.7 1.0
CE1 A:HIS474 4.4 36.3 1.0
CG A:ASP311 4.4 34.8 1.0
NE2 A:HIS474 4.4 34.3 1.0
ZN A:ZN903 4.4 38.0 1.0
C20 A:YN2902 4.4 41.1 1.0
CB A:ASP358 4.4 33.3 1.0
N21 A:YN2902 4.5 38.9 1.0
C A:THR209 4.6 42.0 1.0
CA A:ASP171 4.6 34.9 1.0
C A:LYS208 4.7 41.8 1.0
OD2 A:ASP311 4.8 35.8 1.0
C A:ASP171 4.8 34.2 1.0
C16 A:YN2902 4.9 43.3 1.0
CB A:ASP311 4.9 35.0 1.0
O A:THR209 5.0 43.1 1.0

Calcium binding site 2 out of 2 in 7g4j

Go back to Calcium Binding Sites List in 7g4j
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[Rac-(E)-3-Oxo-3- [Rac-(3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]Prop-1-Enyl]Benzonitrile, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)C#N)Cn(C2)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.193037 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 4-[Rac-(E)-3-Oxo-3- [Rac-(3AR,8AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A- Octahydropyrrolo[3,4-D]Azepin-6-Yl]Prop-1-Enyl]Benzonitrile, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)C#N)Cn(C2)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.193037 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:43.5
occ:1.00
 OD1 A:ASP739 2.2 43.0 1.0
OD1 A:ASP747 2.2 37.9 1.0
OD1 A:ASN741 2.2 43.6 1.0
O A:HOH1129 2.2 48.1 1.0
O A:LEU745 2.3 42.7 1.0
OD1 A:ASP743 2.3 42.9 1.0
CG A:ASP743 3.1 43.0 1.0
CG A:ASN741 3.2 40.7 1.0
CG A:ASP739 3.3 38.1 1.0
OD2 A:ASP743 3.4 42.4 1.0
C A:LEU745 3.4 40.7 1.0
CG A:ASP747 3.5 42.1 1.0
ND2 A:ASN741 3.6 39.6 1.0
N A:ASP747 3.9 40.1 1.0
N A:LEU745 3.9 35.9 1.0
CA A:ASP739 4.0 39.6 1.0
C A:ARG746 4.0 41.3 1.0
CB A:ASP739 4.1 39.7 1.0
CA A:LEU745 4.2 38.7 1.0
OD2 A:ASP739 4.2 36.3 1.0
OD2 A:ASP747 4.2 49.8 1.0
N A:ASP743 4.2 44.7 1.0
O A:ARG746 4.3 41.9 1.0
CA A:ASP747 4.3 38.8 1.0
CB A:ASP743 4.4 41.4 1.0
N A:ARG746 4.4 39.5 1.0
CB A:ASP747 4.5 39.2 1.0
CB A:LEU745 4.5 38.5 1.0
O A:PHE738 4.6 35.3 1.0
C A:ASP739 4.6 38.5 1.0
N A:ASN741 4.6 42.2 1.0
CB A:ASN741 4.6 41.4 1.0
CA A:ARG746 4.6 41.4 1.0
N A:GLY744 4.7 39.0 1.0
CA A:ASP743 4.7 42.2 1.0
N A:TYR742 4.8 43.7 1.0
C A:ASN741 4.8 45.0 1.0
C A:ASP743 4.9 40.0 1.0
CA A:ASN741 4.9 43.3 1.0
N A:TYR740 4.9 39.9 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 15:46:26 2025

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