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Zinc in PDB 7g5l: Crystal Structure of Rat Autotaxin in Complex with Rac-(3AR,8AS)-6- [Rac-(E)-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-Enoyl]-N-(1H-Triazol-5- Ylmethyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2- Carboxamide, I.E. Smiles C1C(Ccc(C1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1) Cn(C2)C(=O)NCC1=Cn=NN1)Oc(F)(F)F with IC50=0.493964 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(3AR,8AS)-6- [Rac-(E)-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-Enoyl]-N-(1H-Triazol-5- Ylmethyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2- Carboxamide, I.E. Smiles C1C(Ccc(C1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1) Cn(C2)C(=O)NCC1=Cn=NN1)Oc(F)(F)F with IC50=0.493964 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(3AR,8AS)-6- [Rac-(E)-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-Enoyl]-N-(1H-Triazol-5- Ylmethyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2- Carboxamide, I.E. Smiles C1C(Ccc(C1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1) Cn(C2)C(=O)NCC1=Cn=NN1)Oc(F)(F)F with IC50=0.493964 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(3AR,8AS)-6- [Rac-(E)-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-Enoyl]-N-(1H-Triazol-5- Ylmethyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2- Carboxamide, I.E. Smiles C1C(Ccc(C1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1) Cn(C2)C(=O)NCC1=Cn=NN1)Oc(F)(F)F with IC50=0.493964 Microm, PDB code: 7g5l was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.87 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.072, 93.744, 121.251, 90, 90, 90
R / Rfree (%) 20.7 / 26.3

Other elements in 7g5l:

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(3AR,8AS)-6- [Rac-(E)-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-Enoyl]-N-(1H-Triazol-5- Ylmethyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2- Carboxamide, I.E. Smiles C1C(Ccc(C1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1) Cn(C2)C(=O)NCC1=Cn=NN1)Oc(F)(F)F with IC50=0.493964 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Fluorine (F) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin in Complex with Rac-(3AR,8AS)-6- [Rac-(E)-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-Enoyl]-N-(1H-Triazol-5- Ylmethyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2- Carboxamide, I.E. Smiles C1C(Ccc(C1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1) Cn(C2)C(=O)NCC1=Cn=NN1)Oc(F)(F)F with IC50=0.493964 Microm (pdb code 7g5l). 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-(3AR,8AS)-6- [Rac-(E)-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-Enoyl]-N-(1H-Triazol-5- Ylmethyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2- Carboxamide, I.E. Smiles C1C(Ccc(C1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1) Cn(C2)C(=O)NCC1=Cn=NN1)Oc(F)(F)F with IC50=0.493964 Microm, PDB code: 7g5l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7g5l

Go back to Zinc Binding Sites List in 7g5l
Zinc binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(3AR,8AS)-6- [Rac-(E)-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-Enoyl]-N-(1H-Triazol-5- Ylmethyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2- Carboxamide, I.E. Smiles C1C(Ccc(C1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1) Cn(C2)C(=O)NCC1=Cn=NN1)Oc(F)(F)F with IC50=0.493964 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-(3AR,8AS)-6- [Rac-(E)-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-Enoyl]-N-(1H-Triazol-5- Ylmethyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2- Carboxamide, I.E. Smiles C1C(Ccc(C1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1) Cn(C2)C(=O)NCC1=Cn=NN1)Oc(F)(F)F with IC50=0.493964 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn905

b:44.9
occ:1.00
 OD1 A:ASP311 2.0 53.5 1.0
NE2 A:HIS315 2.0 54.1 1.0
N33 A:XV2901 2.1 71.0 1.0
NE2 A:HIS474 2.1 57.5 1.0
N34 A:XV2901 2.3 74.4 1.0
OD2 A:ASP311 2.5 54.1 1.0
CG A:ASP311 2.5 50.1 1.0
CE1 A:HIS315 3.0 53.8 1.0
CD2 A:HIS474 3.0 54.8 1.0
CD2 A:HIS315 3.0 53.8 1.0
CE1 A:HIS474 3.1 54.8 1.0
C32 A:XV2901 3.1 80.8 1.0
N35 A:XV2901 3.4 77.6 1.0
C36 A:XV2901 3.8 78.4 1.0
C31 A:XV2901 4.0 86.9 1.0
CB A:ASP311 4.0 48.2 1.0
ND1 A:HIS315 4.1 53.4 1.0
CG A:HIS315 4.2 52.9 1.0
CG A:HIS474 4.2 52.2 1.0
ND1 A:HIS474 4.2 53.7 1.0
CE1 A:HIS359 4.3 44.5 1.0
OG1 A:THR209 4.5 45.6 1.0
NE2 A:HIS359 4.5 44.3 1.0
CE A:MET361 4.6 49.2 1.0
ZN A:ZN906 4.8 46.9 1.0
OD1 A:ASP171 4.8 47.1 1.0
CA A:ASP311 4.9 47.3 1.0
O A:ASP311 5.0 48.6 1.0

Zinc binding site 2 out of 2 in 7g5l

Go back to Zinc Binding Sites List in 7g5l
Zinc binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(3AR,8AS)-6- [Rac-(E)-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-Enoyl]-N-(1H-Triazol-5- Ylmethyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2- Carboxamide, I.E. Smiles C1C(Ccc(C1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1) Cn(C2)C(=O)NCC1=Cn=NN1)Oc(F)(F)F with IC50=0.493964 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-(3AR,8AS)-6- [Rac-(E)-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-Enoyl]-N-(1H-Triazol-5- Ylmethyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2- Carboxamide, I.E. Smiles C1C(Ccc(C1)/C=C/C(=O)N1CC[C@@H]2[C@H](CC1) Cn(C2)C(=O)NCC1=Cn=NN1)Oc(F)(F)F with IC50=0.493964 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn906

b:46.9
occ:1.00
 OD1 A:ASP171 1.8 47.1 1.0
OD2 A:ASP358 2.0 44.0 1.0
OG1 A:THR209 2.0 45.6 1.0
NE2 A:HIS359 2.1 44.3 1.0
CG A:ASP171 2.6 48.8 1.0
OD2 A:ASP171 2.8 48.7 1.0
CB A:THR209 2.8 46.8 1.0
CG A:ASP358 2.9 43.2 1.0
CE1 A:HIS359 3.0 44.5 1.0
CD2 A:HIS359 3.0 43.8 1.0
CG2 A:THR209 3.0 47.9 1.0
OD1 A:ASP358 3.1 44.5 1.0
CA A:THR209 3.3 47.1 1.0
N A:THR209 3.9 47.5 1.0
CB A:ASP171 4.0 48.3 1.0
ND1 A:HIS359 4.0 44.3 1.0
CG A:HIS359 4.0 43.7 1.0
N33 A:XV2901 4.2 71.0 1.0
CB A:ASP358 4.3 41.4 1.0
CA A:ASP171 4.4 47.7 1.0
N A:GLY172 4.4 46.8 1.0
OD1 A:ASP311 4.5 53.5 1.0
CE1 A:HIS474 4.6 54.8 1.0
CG A:ASP311 4.6 50.1 1.0
C A:THR209 4.6 47.6 1.0
NE2 A:HIS474 4.6 57.5 1.0
C A:LYS208 4.7 46.0 1.0
ZN A:ZN905 4.8 44.9 1.0
C A:ASP171 4.8 47.0 1.0
OD2 A:ASP311 4.9 54.1 1.0
CB A:ASP311 4.9 48.2 1.0
O A:THR209 5.0 47.5 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 00:30:45 2025

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