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Chlorine 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:

Zinc (Zn) 1 atom
Sodium (Na) 2 atoms
Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7g42

Go back to Chlorine Binding Sites List in 7g42
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl901

b:35.1
occ:1.00
 CL23 A:Y23901 0.0 35.1 1.0
C10 A:Y23901 1.7 29.9 1.0
C11 A:Y23901 2.7 29.0 1.0
C13 A:Y23901 2.7 31.0 1.0
NE1 A:TRP254 3.6 54.1 1.0
CB A:PHE210 3.7 30.8 1.0
O A:PHE210 3.8 25.9 1.0
CG2 A:ILE227 3.9 21.6 1.0
CG1 A:ILE227 4.0 25.3 1.0
C07 A:Y23901 4.0 27.5 1.0
C12 A:Y23901 4.1 28.1 1.0
CB A:TYR214 4.1 24.1 1.0
CG A:PHE210 4.1 36.8 1.0
CA A:PHE210 4.2 28.2 1.0
C A:PHE210 4.3 23.8 1.0
CB A:ILE227 4.4 23.5 1.0
CD1 A:TRP254 4.5 49.6 1.0
CE2 A:TRP254 4.5 52.0 1.0
C08 A:Y23901 4.5 28.9 1.0
CG A:TYR214 4.5 23.2 1.0
CD2 A:PHE210 4.6 46.2 1.0
CD1 A:ILE227 4.6 27.6 1.0
CD1 A:PHE210 4.7 37.1 1.0
CZ2 A:TRP254 4.8 56.4 1.0
CZ A:PHE241 4.9 34.5 1.0
CD1 A:TYR214 4.9 24.1 1.0

Chlorine binding site 2 out of 2 in 7g42

Go back to Chlorine Binding Sites List in 7g42
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl903

b:46.5
occ:1.00
 N A:ASN230 3.3 29.7 1.0
NH1 A:ARG391 3.4 35.2 1.0
CA A:GLY229 3.5 26.9 1.0
N A:SER231 3.7 31.2 1.0
C A:GLY229 3.9 29.3 1.0
O A:SER231 4.0 36.8 1.0
CE A:LYS208 4.1 33.9 1.0
CA A:ASN230 4.2 32.2 1.0
CG1 A:VAL385 4.2 33.2 1.0
CB A:ASN230 4.3 33.1 1.0
CG A:LYS208 4.4 27.1 1.0
CZ A:ARG391 4.4 34.5 1.0
CD2 A:LEU389 4.4 42.9 1.0
C A:ASN230 4.5 32.8 1.0
NH2 A:ARG391 4.5 31.1 1.0
CA A:SER231 4.6 34.1 1.0
CB A:SER231 4.6 37.3 1.0
CD1 A:LEU389 4.7 40.2 1.0
C A:SER231 4.8 37.5 1.0
CD A:LYS208 4.8 31.4 1.0
CG A:LEU389 4.8 36.3 1.0
N A:GLY229 4.9 25.9 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 16:54:57 2025

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