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Calcium in PDB 7g7o: Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm, PDB code: 7g7o 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) 45.61 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.911, 91.222, 118.633, 90, 90, 90
R / Rfree (%) 18.7 / 23.9

Other elements in 7g7o:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Potassium (K) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm (pdb code 7g7o). 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 3-Methyl-5-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm, PDB code: 7g7o:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g7o

Go back to Calcium Binding Sites List in 7g7o
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 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 3-Methyl-5-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:42.3
occ:1.00
 OD1 A:ASP171 1.9 35.2 1.0
OG1 A:THR209 1.9 32.2 1.0
NE2 A:HIS359 2.1 27.1 1.0
OD2 A:ASP358 2.2 34.6 1.0
CG A:ASP171 2.8 37.4 1.0
CE1 A:HIS359 2.9 25.5 1.0
CB A:THR209 2.9 30.2 1.0
CD2 A:HIS359 3.0 28.2 1.0
OD2 A:ASP171 3.1 46.9 1.0
CG A:ASP358 3.1 33.5 1.0
CG2 A:THR209 3.3 28.8 1.0
CA A:THR209 3.3 27.9 1.0
OD1 A:ASP358 3.4 26.1 1.0
N A:THR209 3.8 28.6 1.0
ND1 A:HIS359 4.0 27.5 1.0
C33 A:Y3K902 4.0 47.3 1.0
CG A:HIS359 4.1 27.0 1.0
CB A:ASP171 4.1 33.8 1.0
OD1 A:ASP311 4.1 33.0 1.0
N A:GLY172 4.3 30.6 1.0
CE1 A:HIS474 4.3 27.9 1.0
CB A:ASP358 4.4 27.9 1.0
CA A:ASP171 4.4 31.2 1.0
CG A:ASP311 4.4 34.7 1.0
O A:HOH1001 4.4 43.9 1.0
NE2 A:HIS474 4.5 26.9 1.0
ZN A:ZN906 4.5 34.6 1.0
N39 A:Y3K902 4.5 45.2 1.0
C34 A:Y3K902 4.6 56.2 1.0
C A:THR209 4.6 31.0 1.0
C A:LYS208 4.7 30.2 1.0
C A:ASP171 4.7 31.6 1.0
CB A:ASP311 4.8 32.3 1.0
OD2 A:ASP311 4.9 37.8 1.0

Calcium binding site 2 out of 2 in 7g7o

Go back to Calcium Binding Sites List in 7g7o
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 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 3-Methyl-5-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:27.8
occ:1.00
 OD1 A:ASP747 2.2 30.9 1.0
OD1 A:ASP743 2.3 31.1 1.0
O A:LEU745 2.3 26.1 1.0
OD1 A:ASN741 2.3 29.1 1.0
OD1 A:ASP739 2.3 24.2 1.0
O A:HOH1206 2.3 30.3 1.0
CG A:ASP743 3.2 31.1 1.0
CG A:ASN741 3.4 30.8 1.0
CG A:ASP747 3.4 32.1 1.0
C A:LEU745 3.4 28.8 1.0
CG A:ASP739 3.5 26.5 1.0
OD2 A:ASP743 3.6 32.9 1.0
ND2 A:ASN741 3.9 30.9 1.0
N A:ASP747 3.9 26.1 1.0
C A:ARG746 4.0 27.2 1.0
N A:LEU745 4.0 26.1 1.0
CA A:ASP739 4.0 28.5 1.0
CA A:ASP747 4.1 28.1 1.0
O A:ARG746 4.1 27.9 1.0
CA A:LEU745 4.2 27.8 1.0
N A:ASP743 4.2 29.9 1.0
OD2 A:ASP747 4.2 31.2 1.0
CB A:ASP739 4.3 25.1 1.0
CB A:ASP747 4.4 30.9 1.0
OD2 A:ASP739 4.4 24.3 1.0
O A:PHE738 4.4 26.3 1.0
N A:ASN741 4.4 26.6 1.0
CB A:LEU745 4.4 26.9 1.0
CB A:ASP743 4.5 27.0 1.0
N A:ARG746 4.5 26.2 1.0
C A:ASP739 4.5 28.1 1.0
CB A:ASN741 4.7 27.1 1.0
N A:TYR742 4.7 27.0 1.0
CA A:ARG746 4.7 28.0 1.0
N A:GLY744 4.7 29.3 1.0
N A:TYR740 4.8 27.7 1.0
CA A:ASP743 4.8 29.8 1.0
OE2 A:GLU751 4.8 44.1 1.0
C A:ASN741 4.9 29.0 1.0
CA A:ASN741 4.9 27.3 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 22:39:13 2025

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