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Sodium in PDB 7g42: Crystal Structure of Rat Autotaxin in Complex with 4-[[6-Chloro-2-[3- (1H-Imidazol-5-Yl)Propanoyl]-3,4-Dihydro-1H-Pyrido[3,4-B]Indol-9- Yl]Methyl]Benzonitrile, I.E. Smiles C12=C(Cn(CC1)C(=O)CCC1=Cn=CN1) N(C1C2CC(CC1)Cl)CC1CCC(CC1)C#N with IC50=1.37998 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[[6-Chloro-2-[3- (1H-Imidazol-5-Yl)Propanoyl]-3,4-Dihydro-1H-Pyrido[3,4-B]Indol-9- Yl]Methyl]Benzonitrile, I.E. Smiles C12=C(Cn(CC1)C(=O)CCC1=Cn=CN1) N(C1C2CC(CC1)Cl)CC1CCC(CC1)C#N with IC50=1.37998 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[[6-Chloro-2-[3- (1H-Imidazol-5-Yl)Propanoyl]-3,4-Dihydro-1H-Pyrido[3,4-B]Indol-9- Yl]Methyl]Benzonitrile, I.E. Smiles C12=C(Cn(CC1)C(=O)CCC1=Cn=CN1) N(C1C2CC(CC1)Cl)CC1CCC(CC1)C#N with IC50=1.37998 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[[6-Chloro-2-[3- (1H-Imidazol-5-Yl)Propanoyl]-3,4-Dihydro-1H-Pyrido[3,4-B]Indol-9- Yl]Methyl]Benzonitrile, I.E. Smiles C12=C(Cn(CC1)C(=O)CCC1=Cn=CN1) N(C1C2CC(CC1)Cl)CC1CCC(CC1)C#N with IC50=1.37998 Microm, PDB code: 7g42 was solved by M.Stihle, J.Benz, D.Hunziker, K.Masubuchi, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.70 / 2.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.551, 91.399, 118.762, 90, 90, 90
R / Rfree (%) 18.5 / 23.2

Other elements in 7g42:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[[6-Chloro-2-[3- (1H-Imidazol-5-Yl)Propanoyl]-3,4-Dihydro-1H-Pyrido[3,4-B]Indol-9- Yl]Methyl]Benzonitrile, I.E. Smiles C12=C(Cn(CC1)C(=O)CCC1=Cn=CN1) N(C1C2CC(CC1)Cl)CC1CCC(CC1)C#N with IC50=1.37998 Microm also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-[[6-Chloro-2-[3- (1H-Imidazol-5-Yl)Propanoyl]-3,4-Dihydro-1H-Pyrido[3,4-B]Indol-9- Yl]Methyl]Benzonitrile, I.E. Smiles C12=C(Cn(CC1)C(=O)CCC1=Cn=CN1) N(C1C2CC(CC1)Cl)CC1CCC(CC1)C#N with IC50=1.37998 Microm (pdb code 7g42). 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 4-[[6-Chloro-2-[3- (1H-Imidazol-5-Yl)Propanoyl]-3,4-Dihydro-1H-Pyrido[3,4-B]Indol-9- Yl]Methyl]Benzonitrile, I.E. Smiles C12=C(Cn(CC1)C(=O)CCC1=Cn=CN1) N(C1C2CC(CC1)Cl)CC1CCC(CC1)C#N with IC50=1.37998 Microm, PDB code: 7g42:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g42

Go back to Sodium Binding Sites List in 7g42
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[[6-Chloro-2-[3- (1H-Imidazol-5-Yl)Propanoyl]-3,4-Dihydro-1H-Pyrido[3,4-B]Indol-9- Yl]Methyl]Benzonitrile, I.E. Smiles C12=C(Cn(CC1)C(=O)CCC1=Cn=CN1) N(C1C2CC(CC1)Cl)CC1CCC(CC1)C#N with IC50=1.37998 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 4-[[6-Chloro-2-[3- (1H-Imidazol-5-Yl)Propanoyl]-3,4-Dihydro-1H-Pyrido[3,4-B]Indol-9- Yl]Methyl]Benzonitrile, I.E. Smiles C12=C(Cn(CC1)C(=O)CCC1=Cn=CN1) N(C1C2CC(CC1)Cl)CC1CCC(CC1)C#N with IC50=1.37998 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:58.6
occ:1.00
 O A:HOH1186 2.4 49.7 1.0
O A:HOH1270 2.7 44.4 1.0
O A:CYS568 2.7 51.1 1.0
OD1 A:ASP570 2.9 62.5 1.0
C A:CYS568 3.8 52.1 1.0
CG A:ASP570 4.1 68.7 1.0
NE2 A:GLN559 4.1 45.3 1.0
N A:CYS568 4.2 44.5 1.0
CA A:CYS568 4.4 47.1 1.0
CB A:LYS571 4.5 80.0 1.0
CB A:CYS568 4.6 45.3 1.0
OD2 A:ASP570 4.6 62.2 1.0
N A:ASP570 4.6 63.3 1.0
N A:LYS571 4.7 78.3 1.0
N A:ASP569 5.0 59.8 1.0

Sodium binding site 2 out of 2 in 7g42

Go back to Sodium Binding Sites List in 7g42
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[[6-Chloro-2-[3- (1H-Imidazol-5-Yl)Propanoyl]-3,4-Dihydro-1H-Pyrido[3,4-B]Indol-9- Yl]Methyl]Benzonitrile, I.E. Smiles C12=C(Cn(CC1)C(=O)CCC1=Cn=CN1) N(C1C2CC(CC1)Cl)CC1CCC(CC1)C#N with IC50=1.37998 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 4-[[6-Chloro-2-[3- (1H-Imidazol-5-Yl)Propanoyl]-3,4-Dihydro-1H-Pyrido[3,4-B]Indol-9- Yl]Methyl]Benzonitrile, I.E. Smiles C12=C(Cn(CC1)C(=O)CCC1=Cn=CN1) N(C1C2CC(CC1)Cl)CC1CCC(CC1)C#N with IC50=1.37998 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:38.9
occ:1.00
 O A:SER804 2.3 29.4 1.0
OG A:SER807 2.3 31.8 1.0
O A:HOH1197 2.3 29.0 1.0
O A:HOH1268 2.5 46.3 1.0
O A:ASN801 2.5 28.9 1.0
O A:HOH1233 2.6 36.6 1.0
C A:SER804 3.4 31.5 1.0
CB A:SER807 3.4 31.8 1.0
C A:ASN801 3.4 30.5 1.0
CA A:ASP802 3.9 30.1 1.0
N A:SER807 4.0 34.4 1.0
N A:ASP802 4.1 30.3 1.0
O A:CYS805 4.1 40.6 1.0
CA A:CYS805 4.2 37.1 1.0
O A:ASP802 4.2 29.7 1.0
N A:CYS805 4.2 32.6 1.0
C A:CYS805 4.2 40.3 1.0
C A:ASP802 4.2 29.0 1.0
CA A:SER807 4.2 35.3 1.0
N A:SER804 4.3 28.7 1.0
CA A:SER804 4.3 28.3 1.0
CB A:ASN801 4.4 30.1 1.0
CA A:ASN801 4.5 31.7 1.0
O A:HOH1152 4.7 35.0 1.0
OD1 A:ASP802 4.7 41.1 1.0
CB A:SER804 4.7 31.9 1.0
N A:ASN806 4.9 39.9 1.0
C A:SER807 4.9 37.9 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 23:17:20 2025

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