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Zinc in PDB 7g5m: Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm, PDB code: 7g5m 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) 46.08 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.348, 92.166, 120.549, 90, 90, 90
R / Rfree (%) 20.1 / 24.4

Other elements in 7g5m:

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm (pdb code 7g5m). 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 Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm, PDB code: 7g5m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7g5m

Go back to Zinc Binding Sites List in 7g5m
Zinc binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 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 Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:25.4
occ:1.00
 OG1 A:THR209 1.7 20.5 1.0
OD1 A:ASP171 1.9 22.6 1.0
OD2 A:ASP358 2.1 23.8 1.0
NE2 A:HIS359 2.1 20.4 1.0
CG A:ASP171 2.6 23.8 1.0
OD2 A:ASP171 2.8 22.8 1.0
CD2 A:HIS359 2.9 18.4 1.0
CB A:THR209 2.9 22.2 1.0
CG A:ASP358 3.0 24.6 1.0
CE1 A:HIS359 3.2 20.8 1.0
OD1 A:ASP358 3.2 24.6 1.0
CA A:THR209 3.4 21.0 1.0
CG2 A:THR209 3.4 20.8 1.0
N A:THR209 3.9 23.0 1.0
CB A:ASP171 4.0 23.9 1.0
CG A:HIS359 4.1 20.9 1.0
O A:HOH1160 4.1 27.2 1.0
ND1 A:HIS359 4.2 18.6 1.0
N A:GLY172 4.2 24.9 1.0
OD1 A:ASP311 4.2 25.9 1.0
C32 A:Y0F902 4.2 34.9 1.0
CA A:ASP171 4.3 25.5 1.0
CB A:ASP358 4.3 22.6 1.0
CE1 A:HIS474 4.4 20.5 1.0
CG A:ASP311 4.5 23.4 1.0
C A:ASP171 4.6 25.5 1.0
NE2 A:HIS474 4.7 21.8 1.0
ZN A:ZN904 4.7 25.3 1.0
C35 A:Y0F902 4.7 32.6 1.0
C A:LYS208 4.8 22.8 1.0
C A:THR209 4.8 21.4 1.0
N36 A:Y0F902 4.8 35.5 1.0
CB A:ASP311 4.9 24.5 1.0

Zinc binding site 2 out of 2 in 7g5m

Go back to Zinc Binding Sites List in 7g5m
Zinc binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 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 Rac-(E)-1-[Rac- (3AR,8AS)-2-(1,4,6,7-Tetrahydrotriazolo[4,5-C]Pyridine-5-Carbonyl)-1, 3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-6-Yl]-3-[4- (Trifluoromethoxy)Phenyl]Prop-2-En-1-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F)Cn(C2)C(=O) N1CCC2=C(C1)N=NN2 with IC50=0.0280543 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:25.3
occ:1.00
 N36 A:Y0F902 1.7 35.5 1.0
OD1 A:ASP311 1.9 25.9 1.0
NE2 A:HIS315 2.1 27.1 1.0
NE2 A:HIS474 2.1 21.8 1.0
OD2 A:ASP311 2.6 30.2 1.0
CG A:ASP311 2.6 23.4 1.0
N37 A:Y0F902 2.6 36.0 1.0
C35 A:Y0F902 2.9 32.6 1.0
CD2 A:HIS315 3.0 25.6 1.0
CD2 A:HIS474 3.0 20.2 1.0
CE1 A:HIS474 3.2 20.5 1.0
CE1 A:HIS315 3.2 27.0 1.0
C32 A:Y0F902 3.7 34.9 1.0
N38 A:Y0F902 3.9 35.1 1.0
C34 A:Y0F902 4.0 34.4 1.0
O A:HOH1160 4.0 27.2 1.0
CB A:ASP311 4.1 24.5 1.0
CE1 A:HIS359 4.2 20.8 1.0
CG A:HIS315 4.2 24.9 1.0
CG A:HIS474 4.2 19.3 1.0
ND1 A:HIS315 4.2 26.6 1.0
ND1 A:HIS474 4.2 19.9 1.0
O A:HOH1110 4.3 30.7 1.0
CE A:MET361 4.4 25.0 1.0
NE2 A:HIS359 4.4 20.4 1.0
OD1 A:ASP171 4.5 22.6 1.0
OG1 A:THR209 4.7 20.5 1.0
ZN A:ZN901 4.7 25.4 1.0
O A:ASP311 4.9 26.4 1.0
CA A:ASP311 4.9 24.7 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 00:30:45 2025

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