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Zinc 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
Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7g4f

Go back to Zinc Binding Sites List in 7g4f
Zinc 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 Zinc with other atoms in the Zn 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:Zn903

b:23.5
occ:1.00
 OD2 A:ASP311 2.0 26.8 1.0
N19 A:YNX902 2.0 23.7 1.0
NE2 A:HIS315 2.0 20.5 1.0
NE2 A:HIS474 2.1 23.0 1.0
OD1 A:ASP311 2.6 22.0 1.0
CG A:ASP311 2.6 22.6 1.0
N20 A:YNX902 2.8 26.7 1.0
CD2 A:HIS315 2.9 21.4 1.0
CD2 A:HIS474 3.0 19.4 1.0
CE1 A:HIS315 3.0 22.1 1.0
C18 A:YNX902 3.1 25.9 1.0
CE1 A:HIS474 3.2 19.5 1.0
C15 A:YNX902 3.8 24.9 1.0
O A:HOH1073 4.1 20.7 1.0
N21 A:YNX902 4.1 26.9 1.0
CG A:HIS315 4.1 21.1 1.0
CE1 A:HIS359 4.1 21.6 1.0
CB A:ASP311 4.1 20.7 1.0
ND1 A:HIS315 4.1 21.2 1.0
C17 A:YNX902 4.2 26.8 1.0
CG A:HIS474 4.2 18.8 1.0
ND1 A:HIS474 4.2 19.4 1.0
NE2 A:HIS359 4.3 24.1 1.0
O A:HOH1061 4.3 41.5 1.0
CE A:MET361 4.5 21.0 1.0
OD1 A:ASP171 4.5 20.6 1.0
ZN A:ZN904 4.6 22.9 1.0
OG1 A:THR209 4.6 24.1 1.0
O A:ASP311 4.9 21.9 1.0
CA A:ASP311 4.9 19.9 1.0

Zinc binding site 2 out of 2 in 7g4f

Go back to Zinc Binding Sites List in 7g4f
Zinc 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 Zinc with other atoms in the Zn 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:Zn904

b:22.9
occ:1.00
 OG1 A:THR209 1.9 24.1 1.0
OD1 A:ASP171 2.0 20.6 1.0
NE2 A:HIS359 2.1 24.1 1.0
OD2 A:ASP358 2.2 19.8 1.0
CG A:ASP171 2.7 21.2 1.0
CD2 A:HIS359 2.8 18.8 1.0
OD2 A:ASP171 2.9 24.2 1.0
CB A:THR209 3.0 23.2 1.0
CG A:ASP358 3.0 19.8 1.0
CE1 A:HIS359 3.1 21.6 1.0
OD1 A:ASP358 3.2 19.2 1.0
CG2 A:THR209 3.3 22.9 1.0
CA A:THR209 3.4 24.4 1.0
OD2 A:ASP311 3.8 26.8 1.0
O A:HOH1073 4.0 20.7 1.0
N A:THR209 4.0 22.7 1.0
CG A:HIS359 4.0 20.7 1.0
C15 A:YNX902 4.1 24.9 1.0
CB A:ASP171 4.1 19.4 1.0
ND1 A:HIS359 4.1 20.4 1.0
N A:GLY172 4.2 22.4 1.0
CE1 A:HIS474 4.2 19.5 1.0
CB A:ASP358 4.4 19.4 1.0
CA A:ASP171 4.4 20.9 1.0
CG A:ASP311 4.4 22.6 1.0
NE2 A:HIS474 4.5 23.0 1.0
C18 A:YNX902 4.5 25.9 1.0
ZN A:ZN903 4.6 23.5 1.0
N19 A:YNX902 4.6 23.7 1.0
C A:ASP171 4.7 22.6 1.0
C A:LYS208 4.7 23.3 1.0
C A:THR209 4.7 23.8 1.0
C14 A:YNX902 4.9 28.6 1.0
CB A:ASP311 4.9 20.7 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 00:26:19 2025

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