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Sodium in PDB 7g6o: Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[5- Cyclopropyl-6-(Oxan-4-Yloxy)Pyridine-3-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C(NC1)OC1CCOCC1) C1CC1)C(=O)C1NCC(CC1)S(=O)(=O)N with IC50=0.0360867 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[5- Cyclopropyl-6-(Oxan-4-Yloxy)Pyridine-3-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C(NC1)OC1CCOCC1) C1CC1)C(=O)C1NCC(CC1)S(=O)(=O)N with IC50=0.0360867 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[5- Cyclopropyl-6-(Oxan-4-Yloxy)Pyridine-3-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C(NC1)OC1CCOCC1) C1CC1)C(=O)C1NCC(CC1)S(=O)(=O)N with IC50=0.0360867 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[5- Cyclopropyl-6-(Oxan-4-Yloxy)Pyridine-3-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C(NC1)OC1CCOCC1) C1CC1)C(=O)C1NCC(CC1)S(=O)(=O)N with IC50=0.0360867 Microm, PDB code: 7g6o 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) 48.93 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.79, 91.977, 119.81, 90, 90, 90
R / Rfree (%) 19.2 / 24.5

Other elements in 7g6o:

The structure of Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[5- Cyclopropyl-6-(Oxan-4-Yloxy)Pyridine-3-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C(NC1)OC1CCOCC1) C1CC1)C(=O)C1NCC(CC1)S(=O)(=O)N with IC50=0.0360867 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[5- Cyclopropyl-6-(Oxan-4-Yloxy)Pyridine-3-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C(NC1)OC1CCOCC1) C1CC1)C(=O)C1NCC(CC1)S(=O)(=O)N with IC50=0.0360867 Microm (pdb code 7g6o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[5- Cyclopropyl-6-(Oxan-4-Yloxy)Pyridine-3-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C(NC1)OC1CCOCC1) C1CC1)C(=O)C1NCC(CC1)S(=O)(=O)N with IC50=0.0360867 Microm, PDB code: 7g6o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g6o

Go back to Sodium Binding Sites List in 7g6o
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[5- Cyclopropyl-6-(Oxan-4-Yloxy)Pyridine-3-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C(NC1)OC1CCOCC1) C1CC1)C(=O)C1NCC(CC1)S(=O)(=O)N with IC50=0.0360867 Microm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[5- Cyclopropyl-6-(Oxan-4-Yloxy)Pyridine-3-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C(NC1)OC1CCOCC1) C1CC1)C(=O)C1NCC(CC1)S(=O)(=O)N with IC50=0.0360867 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:44.1
occ:1.00
 OG A:SER807 2.3 37.0 1.0
O A:SER804 2.3 36.4 1.0
O A:HOH1278 2.3 47.5 1.0
O A:HOH1105 2.4 45.7 1.0
O A:HOH1189 2.5 43.0 1.0
O A:ASN801 2.6 34.2 1.0
C A:ASN801 3.4 34.6 1.0
C A:SER804 3.4 37.9 1.0
CB A:SER807 3.5 42.5 1.0
CA A:ASP802 3.9 38.1 1.0
N A:ASP802 4.0 35.4 1.0
N A:SER807 4.1 44.5 1.0
O A:ASP802 4.2 36.3 1.0
C A:ASP802 4.2 38.4 1.0
N A:CYS805 4.3 41.4 1.0
CA A:CYS805 4.3 47.1 1.0
CA A:SER807 4.3 46.0 1.0
N A:SER804 4.3 35.9 1.0
CA A:SER804 4.3 35.2 1.0
CB A:ASN801 4.4 34.1 1.0
C A:CYS805 4.4 46.4 1.0
O A:CYS805 4.4 45.7 1.0
CA A:ASN801 4.5 34.5 1.0
OD1 A:ASP802 4.7 48.2 1.0
CB A:SER804 4.7 34.8 1.0
O A:HOH1227 4.9 34.5 1.0
N A:ASN806 4.9 49.0 1.0

Sodium binding site 2 out of 2 in 7g6o

Go back to Sodium Binding Sites List in 7g6o
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[5- Cyclopropyl-6-(Oxan-4-Yloxy)Pyridine-3-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C(NC1)OC1CCOCC1) C1CC1)C(=O)C1NCC(CC1)S(=O)(=O)N with IC50=0.0360867 Microm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with 6-[(3AR,6AR)-5-[5- Cyclopropyl-6-(Oxan-4-Yloxy)Pyridine-3-Carbonyl]-1,3,3A,4,6,6A- Hexahydropyrrolo[3,4-C]Pyrrole-2-Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C(NC1)OC1CCOCC1) C1CC1)C(=O)C1NCC(CC1)S(=O)(=O)N with IC50=0.0360867 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:30.4
occ:1.00
 O A:HOH1236 2.1 49.3 1.0
O A:HOH1226 2.2 43.3 1.0
O A:ASP672 2.3 43.2 1.0
O A:MET675 2.3 43.6 1.0
O A:TYR669 2.3 42.0 1.0
O A:HOH1276 2.6 44.1 1.0
C A:MET675 3.5 38.8 1.0
C A:TYR669 3.5 42.3 1.0
C A:ASP672 3.5 45.7 1.0
N A:MET675 4.2 41.8 1.0
O A:LYS670 4.3 44.9 1.0
CA A:TYR669 4.3 38.3 1.0
N A:SER676 4.3 34.3 1.0
CA A:SER676 4.4 33.0 1.0
N A:LYS673 4.4 45.4 1.0
CA A:MET675 4.4 40.4 1.0
CA A:LYS673 4.4 48.8 1.0
CA A:ASP672 4.4 45.6 1.0
C A:LYS673 4.4 45.1 1.0
O A:LYS673 4.5 44.9 1.0
N A:LYS670 4.5 45.9 1.0
N A:ASP672 4.6 51.0 1.0
CB A:ASP672 4.6 47.7 1.0
CB A:TYR669 4.6 36.5 1.0
CA A:LYS670 4.7 47.5 1.0
C A:LYS670 4.7 47.2 1.0
CB A:SER676 4.8 30.8 1.0
C A:GLN674 4.9 46.3 1.0
N A:GLN674 5.0 47.7 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: Sat Feb 8 23:30:32 2025

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