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Calcium in PDB 7g4f: Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm, PDB code: 7g4f 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) 42.87 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.087, 91.718, 119.857, 90, 90, 90
R / Rfree (%) 18.7 / 23.2

Other elements in 7g4f:

The structure of Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm (pdb code 7g4f). 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 (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm, PDB code: 7g4f:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g4f

Go back to Calcium Binding Sites List in 7g4f
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 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 (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:33.2
occ:1.00
 OD1 A:ASP747 2.1 25.6 1.0
O A:LEU745 2.2 31.2 1.0
OD1 A:ASN741 2.3 29.4 1.0
OD1 A:ASP739 2.3 20.9 1.0
O A:HOH1343 2.3 37.6 1.0
OD1 A:ASP743 2.4 26.0 1.0
CG A:ASN741 3.2 29.3 1.0
CG A:ASP747 3.3 27.9 1.0
CG A:ASP743 3.3 27.0 1.0
C A:LEU745 3.4 28.1 1.0
CG A:ASP739 3.4 22.6 1.0
ND2 A:ASN741 3.5 31.2 1.0
OD2 A:ASP743 3.7 28.6 1.0
CA A:ASP739 3.9 22.1 1.0
C A:ARG746 3.9 26.2 1.0
N A:ASP747 3.9 25.2 1.0
O A:ARG746 3.9 24.2 1.0
OD2 A:ASP747 4.1 31.6 1.0
CB A:ASP739 4.1 23.2 1.0
CA A:ASP747 4.1 24.0 1.0
N A:LEU745 4.1 26.0 1.0
CA A:LEU745 4.2 25.4 1.0
O A:PHE738 4.3 21.8 1.0
N A:ASP743 4.3 21.6 1.0
CB A:ASP747 4.3 25.3 1.0
N A:ARG746 4.4 25.6 1.0
C A:ASP739 4.4 23.8 1.0
OD2 A:ASP739 4.4 22.1 1.0
N A:ASN741 4.4 23.8 1.0
CB A:LEU745 4.5 27.5 1.0
CA A:ARG746 4.5 25.5 0.5
CB A:ASP743 4.6 23.9 1.0
CB A:ASN741 4.6 25.1 1.0
CA A:ARG746 4.6 24.1 0.5
N A:TYR740 4.7 25.0 1.0
N A:TYR742 4.7 23.2 1.0
CA A:ASP743 4.8 22.7 1.0
OE2 A:GLU751 4.8 34.9 1.0
CA A:ASN741 4.8 24.8 1.0
C A:ASN741 4.9 26.4 1.0
O A:ASP739 5.0 19.3 1.0
O A:HOH1416 5.0 46.9 1.0
N A:ASP739 5.0 22.4 1.0

Calcium binding site 2 out of 2 in 7g4f

Go back to Calcium Binding Sites List in 7g4f
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 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 (E)-1-[(3AR,6AR)-5- (1H-Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1N(C[C@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O) /C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00118848 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:50.8
occ:1.00
 OG A:SER807 2.3 28.3 1.0
O A:SER804 2.5 21.7 1.0
O A:HOH1142 2.5 30.7 1.0
O A:HOH1422 2.6 38.6 1.0
O A:ASN801 2.6 25.2 1.0
O A:HOH1175 2.7 29.5 1.0
C A:ASN801 3.4 25.4 1.0
CB A:SER807 3.5 30.6 1.0
C A:SER804 3.5 26.4 1.0
CA A:ASP802 3.9 25.2 1.0
O A:HOH1027 4.0 36.4 1.0
N A:ASP802 4.1 24.6 1.0
N A:SER807 4.1 29.8 1.0
O A:ASP802 4.1 23.7 1.0
O A:HOH1478 4.2 45.7 1.0
C A:ASP802 4.2 23.9 1.0
CA A:CYS805 4.2 30.9 1.0
CA A:SER807 4.3 31.9 1.0
N A:CYS805 4.3 27.4 1.0
C A:CYS805 4.4 33.9 1.0
CB A:ASN801 4.4 23.3 1.0
N A:SER804 4.4 23.6 1.0
CA A:ASN801 4.5 23.5 1.0
O A:CYS805 4.5 37.6 1.0
CA A:SER804 4.5 23.0 1.0
O A:HOH1207 4.7 35.8 1.0
OD1 A:ASP802 4.7 29.9 1.0
O A:HOH1074 4.8 42.0 1.0
N A:ASN806 4.9 32.5 1.0
CB A:SER804 4.9 24.3 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: Wed Jul 9 22:25:38 2025

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