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Sodium in PDB 7g2m: Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm, PDB code: 7g2m 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) 48.53 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.891, 91.227, 119.009, 90, 90, 90
R / Rfree (%) 18.9 / 24.5

Other elements in 7g2m:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Fluorine (F) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm (pdb code 7g2m). 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 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm, PDB code: 7g2m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g2m

Go back to Sodium Binding Sites List in 7g2m
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 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 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:55.3
occ:1.00
 O A:HOH1172 2.2 50.0 1.0
OG A:SER807 2.3 51.1 1.0
O A:HOH1013 2.4 34.3 1.0
O A:HOH1171 2.6 48.8 1.0
O A:SER804 2.6 47.4 1.0
O A:ASN801 2.8 35.6 1.0
CB A:SER807 3.6 51.4 1.0
C A:ASN801 3.6 39.0 1.0
C A:SER804 3.7 50.6 1.0
CA A:ASP802 4.0 41.8 1.0
N A:ASP802 4.2 38.9 1.0
N A:SER807 4.2 54.0 1.0
CA A:CYS805 4.3 52.5 1.0
O A:CYS805 4.4 49.6 1.0
C A:ASP802 4.4 44.5 1.0
CA A:SER807 4.4 54.9 1.0
N A:CYS805 4.4 52.5 1.0
O A:ASP802 4.4 44.2 1.0
C A:CYS805 4.4 49.6 1.0
OD1 A:ASP802 4.5 42.5 1.0
CB A:ASN801 4.6 39.5 1.0
CA A:ASN801 4.6 40.7 1.0
CA A:SER804 4.7 49.0 1.0
N A:SER804 4.7 46.6 1.0
C A:SER807 5.0 56.6 1.0

Sodium binding site 2 out of 2 in 7g2m

Go back to Sodium Binding Sites List in 7g2m
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 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 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:33.0
occ:1.00
 O A:HOH1198 2.2 49.3 1.0
O A:ASP672 2.3 47.0 1.0
O A:MET675 2.3 51.1 1.0
O A:TYR669 2.4 51.4 1.0
O A:HOH1217 2.7 57.1 1.0
C A:MET675 3.5 44.9 1.0
C A:ASP672 3.5 49.1 1.0
C A:TYR669 3.6 50.9 1.0
CA A:LYS673 4.2 59.8 1.0
N A:LYS673 4.3 50.7 1.0
N A:SER676 4.3 39.6 1.0
N A:MET675 4.3 52.5 1.0
CA A:SER676 4.3 36.0 1.0
C A:LYS673 4.3 58.0 1.0
O A:LYS673 4.4 57.0 1.0
CA A:TYR669 4.4 47.7 1.0
O A:LYS670 4.4 57.5 1.0
CA A:MET675 4.4 48.1 1.0
N A:LYS670 4.5 54.7 1.0
CA A:ASP672 4.5 50.5 1.0
CA A:LYS670 4.6 58.7 1.0
C A:LYS670 4.7 56.7 1.0
CB A:ASP672 4.8 50.6 1.0
N A:ASP672 4.8 53.6 1.0
CB A:TYR669 4.8 45.8 1.0
CB A:SER676 4.8 35.8 1.0
N A:GLN674 4.9 59.2 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 23:09:26 2025

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