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Calcium in PDB 7g70: Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm, PDB code: 7g70 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) 46.02 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.438, 92.042, 120.427, 90, 90, 90
R / Rfree (%) 20.5 / 24

Other elements in 7g70:

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm (pdb code 7g70). 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 [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm, PDB code: 7g70:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g70

Go back to Calcium Binding Sites List in 7g70
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 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 [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:59.5
occ:1.00
 OG1 A:THR209 2.4 29.1 1.0
NE2 A:HIS359 2.4 18.9 1.0
OD1 A:ASP171 2.4 27.6 1.0
CG2 A:THR209 3.0 22.6 1.0
CB A:THR209 3.0 25.2 1.0
CE1 A:HIS359 3.1 18.3 1.0
CG A:ASP171 3.2 27.5 1.0
OD2 A:ASP171 3.2 30.3 1.0
OD2 A:ASP358 3.3 23.2 1.0
CA A:THR209 3.4 22.0 1.0
ZN A:ZN905 3.5 21.9 1.0
C3 A:Y7A901 3.5 30.5 1.0
CD2 A:HIS359 3.5 18.7 1.0
N7 A:Y7A901 3.6 28.6 1.0
OD1 A:ASP311 3.6 24.8 1.0
CE1 A:HIS474 3.6 21.2 1.0
C6 A:Y7A901 3.6 32.4 1.0
NE2 A:HIS474 3.7 23.8 1.0
N A:THR209 3.8 21.2 1.0
CG A:ASP311 3.9 21.9 1.0
CG A:ASP358 4.1 22.5 1.0
OD2 A:ASP311 4.1 26.7 1.0
OD1 A:ASP358 4.3 19.9 1.0
ND1 A:HIS359 4.4 18.9 1.0
C2 A:Y7A901 4.5 35.0 1.0
ND1 A:HIS474 4.5 20.0 1.0
N8 A:Y7A901 4.6 33.8 1.0
CG A:HIS359 4.6 18.4 1.0
CB A:ASP171 4.6 22.4 1.0
CB A:ASP311 4.6 21.8 1.0
C5 A:Y7A901 4.7 35.5 1.0
CD2 A:HIS474 4.7 20.0 1.0
C A:LYS208 4.8 22.8 1.0
C A:THR209 4.8 21.2 1.0
N A:GLY172 4.8 20.5 1.0

Calcium binding site 2 out of 2 in 7g70

Go back to Calcium Binding Sites List in 7g70
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 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 [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:20.3
occ:1.00
 O A:HOH1337 2.2 22.4 1.0
OD1 A:ASP739 2.2 20.0 1.0
O A:LEU745 2.2 21.1 1.0
OD1 A:ASP747 2.3 22.8 1.0
OD1 A:ASN741 2.4 24.9 1.0
OD1 A:ASP743 2.4 26.4 1.0
CG A:ASP743 3.3 23.7 1.0
CG A:ASP739 3.4 20.6 1.0
C A:LEU745 3.4 21.9 1.0
CG A:ASN741 3.4 25.0 1.0
CG A:ASP747 3.6 23.0 1.0
OD2 A:ASP743 3.7 25.6 1.0
N A:ASP747 3.8 20.4 1.0
ND2 A:ASN741 3.9 24.8 1.0
C A:ARG746 4.0 20.2 1.0
CA A:ASP739 4.0 19.5 1.0
N A:LEU745 4.1 19.8 1.0
CA A:ASP747 4.1 20.9 1.0
CA A:LEU745 4.2 20.2 1.0
CB A:ASP739 4.2 20.0 1.0
O A:ARG746 4.2 23.1 1.0
N A:ASP743 4.3 21.4 1.0
OD2 A:ASP739 4.3 21.4 1.0
O A:PHE738 4.4 20.0 1.0
CB A:ASP747 4.4 20.6 1.0
CB A:LEU745 4.4 22.4 1.0
OD2 A:ASP747 4.4 23.6 1.0
N A:ARG746 4.5 19.9 1.0
N A:ASN741 4.5 23.8 1.0
C A:ASP739 4.5 20.4 1.0
CB A:ASP743 4.5 22.3 1.0
OE2 A:GLU751 4.6 38.2 1.0
CA A:ARG746 4.7 20.1 1.0
N A:TYR740 4.7 20.1 1.0
CB A:ASN741 4.7 23.0 1.0
CA A:ASP743 4.8 22.2 1.0
N A:TYR742 4.8 20.3 1.0
C A:ASN741 4.9 24.3 1.0
CA A:ASN741 4.9 22.3 1.0
N A:GLY744 4.9 20.2 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 15:59:10 2025

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