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Calcium in PDB 7g4p: Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-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 N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-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 N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-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 N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 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-(1H-Benzotriazole-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 N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm, PDB code: 7g4p 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) 46.72 / 2.12
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.786, 93.362, 120.964, 90, 90, 90
R / Rfree (%) 21.8 / 25.8

Other elements in 7g4p:

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-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 N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms
Fluorine (F) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-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 N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm (pdb code 7g4p). 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 Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-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 N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm, PDB code: 7g4p:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g4p

Go back to Calcium Binding Sites List in 7g4p
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-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 N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 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 Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-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 N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:31.8
occ:1.00
 OD1 A:ASP171 1.9 28.0 1.0
OD2 A:ASP358 2.2 28.8 1.0
NE2 A:HIS359 2.2 27.0 1.0
OG1 A:THR209 2.4 32.2 1.0
CG A:ASP171 2.7 27.6 1.0
OD2 A:ASP171 2.8 28.5 1.0
CG2 A:THR209 3.0 31.5 1.0
CB A:THR209 3.0 31.5 1.0
CE1 A:HIS359 3.1 27.6 1.0
CD2 A:HIS359 3.2 27.7 1.0
CG A:ASP358 3.2 28.2 1.0
CA A:THR209 3.4 29.8 1.0
OD1 A:ASP358 3.5 29.0 1.0
OD2 A:ASP311 3.8 26.0 1.0
C17 A:Y6R901 4.0 35.2 1.0
N A:THR209 4.0 29.8 1.0
CB A:ASP171 4.1 27.1 1.0
O A:HOH1002 4.1 38.0 1.0
ND1 A:HIS359 4.2 27.9 1.0
CG A:HIS359 4.2 28.4 1.0
N A:GLY172 4.3 25.4 1.0
CG A:ASP311 4.3 27.7 1.0
ZN A:ZN903 4.3 29.2 1.0
CE1 A:HIS474 4.4 29.7 1.0
CA A:ASP171 4.5 26.3 1.0
NE2 A:HIS474 4.5 29.1 1.0
CB A:ASP358 4.5 27.0 1.0
C20 A:Y6R901 4.5 35.3 1.0
C A:THR209 4.7 28.6 1.0
CB A:ASP311 4.7 28.8 1.0
N21 A:Y6R901 4.7 34.1 1.0
C16 A:Y6R901 4.7 36.6 1.0
C A:ASP171 4.7 26.4 1.0
C A:LYS208 4.8 30.2 1.0

Calcium binding site 2 out of 2 in 7g4p

Go back to Calcium Binding Sites List in 7g4p
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-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 N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 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 Rac-(E)-1-[Rac- (3AR,8AS)-2-(1H-Benzotriazole-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 N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CCC2C(C1)N=NN2)C(=O)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00155284 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:37.4
occ:1.00
 O A:HOH1121 2.0 38.3 1.0
OD1 A:ASP747 2.1 31.7 1.0
O A:LEU745 2.2 28.1 1.0
OD1 A:ASP743 2.3 28.2 1.0
OD1 A:ASN741 2.3 31.0 1.0
OD1 A:ASP739 2.3 29.1 1.0
CG A:ASP743 3.2 28.5 1.0
C A:LEU745 3.3 28.6 1.0
CG A:ASN741 3.3 31.4 1.0
CG A:ASP747 3.4 34.5 1.0
OD2 A:ASP743 3.4 29.3 1.0
CG A:ASP739 3.4 27.9 1.0
ND2 A:ASN741 3.8 34.1 1.0
N A:ASP747 3.9 33.2 1.0
C A:ARG746 3.9 32.7 1.0
N A:LEU745 3.9 27.1 1.0
CA A:ASP739 4.0 28.3 1.0
O A:ARG746 4.1 31.1 1.0
CA A:LEU745 4.1 27.7 1.0
OD2 A:ASP747 4.1 38.6 1.0
CB A:ASP739 4.2 27.3 1.0
CA A:ASP747 4.3 32.3 1.0
OD2 A:ASP739 4.3 28.0 1.0
N A:ARG746 4.3 30.2 1.0
N A:ASP743 4.3 29.3 1.0
CB A:LEU745 4.4 27.2 1.0
CB A:ASP747 4.4 32.7 1.0
CB A:ASP743 4.5 28.4 1.0
O A:PHE738 4.5 27.6 1.0
CA A:ARG746 4.5 32.9 1.0
C A:ASP739 4.6 29.1 1.0
N A:ASN741 4.6 30.1 1.0
CB A:ASN741 4.7 31.5 1.0
N A:TYR742 4.8 34.3 1.0
N A:GLY744 4.8 28.1 1.0
CA A:ASP743 4.8 28.2 1.0
C A:ASN741 4.8 33.7 1.0
CA A:ASN741 4.9 32.4 1.0
N A:TYR740 4.9 28.7 1.0
C A:ASP743 5.0 27.6 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 15:46:32 2025

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