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Calcium 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
Sodium (Na) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 7g42

Go back to Calcium Binding Sites List in 7g42
Calcium 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 Calcium with other atoms in the Ca 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:Ca902

b:24.0
occ:1.00
 OD1 A:ASP747 2.2 26.9 1.0
OD1 A:ASP739 2.2 19.4 1.0
OD1 A:ASN741 2.3 25.7 1.0
O A:LEU745 2.3 22.1 1.0
OD1 A:ASP743 2.3 28.5 1.0
O A:HOH1188 2.4 25.4 1.0
CG A:ASP743 3.2 28.6 1.0
CG A:ASN741 3.3 28.9 1.0
CG A:ASP739 3.4 23.0 1.0
C A:LEU745 3.4 22.6 1.0
CG A:ASP747 3.5 27.7 1.0
OD2 A:ASP743 3.6 28.3 1.0
ND2 A:ASN741 3.7 26.9 1.0
CA A:ASP739 3.9 23.5 1.0
N A:ASP747 3.9 24.2 1.0
N A:LEU745 4.0 22.9 1.0
C A:ARG746 4.1 24.2 1.0
CA A:LEU745 4.1 24.0 1.0
CB A:ASP739 4.2 22.2 1.0
O A:ARG746 4.2 22.9 1.0
CA A:ASP747 4.2 25.1 1.0
N A:ASP743 4.2 26.6 1.0
OD2 A:ASP747 4.3 29.3 1.0
OD2 A:ASP739 4.3 21.7 1.0
CB A:LEU745 4.4 23.5 1.0
N A:ASN741 4.4 23.0 1.0
CB A:ASP747 4.4 24.5 1.0
C A:ASP739 4.4 23.4 1.0
N A:ARG746 4.5 21.3 1.0
O A:PHE738 4.5 23.9 1.0
CB A:ASP743 4.5 25.2 1.0
CB A:ASN741 4.6 23.4 1.0
N A:TYR742 4.6 24.7 1.0
N A:GLY744 4.7 27.6 1.0
CA A:ASP743 4.8 25.8 1.0
CA A:ARG746 4.8 23.7 1.0
N A:TYR740 4.8 23.8 1.0
C A:ASN741 4.8 24.4 1.0
CA A:ASN741 4.9 24.5 1.0
OE2 A:GLU751 4.9 39.6 1.0
C A:ASP743 5.0 26.4 1.0
O A:ASP739 5.0 21.6 1.0

Calcium binding site 2 out of 2 in 7g42

Go back to Calcium Binding Sites List in 7g42
Calcium 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 Calcium with other atoms in the Ca 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:Ca906

b:39.4
occ:1.00
 O A:ACT905 2.1 42.0 1.0
O A:TYR669 2.2 36.2 1.0
O A:ASP672 2.2 34.2 1.0
O A:HOH1211 2.3 46.5 1.0
O A:MET675 2.4 27.8 1.0
O A:HOH1035 2.4 40.2 1.0
C A:TYR669 3.3 35.1 1.0
C A:ACT905 3.3 45.2 1.0
C A:ASP672 3.4 37.5 1.0
C A:MET675 3.5 29.3 1.0
CH3 A:ACT905 4.0 41.3 1.0
O A:LYS670 4.1 46.3 1.0
CA A:TYR669 4.1 30.4 1.0
N A:LYS670 4.2 36.3 1.0
N A:MET675 4.2 33.0 1.0
OXT A:ACT905 4.3 43.8 1.0
N A:LYS673 4.3 36.4 1.0
CA A:LYS673 4.4 39.6 1.0
N A:SER676 4.4 25.9 1.0
CA A:ASP672 4.4 37.0 1.0
CA A:MET675 4.4 29.4 1.0
CA A:SER676 4.4 26.4 1.0
CA A:LYS670 4.4 42.7 1.0
C A:LYS670 4.4 40.4 1.0
C A:LYS673 4.5 39.0 1.0
N A:ASP672 4.5 39.1 1.0
CB A:TYR669 4.5 30.0 1.0
O A:LYS673 4.6 42.8 1.0
CB A:ASP672 4.6 37.1 1.0
N A:GLN674 5.0 41.7 1.0
CB A:SER676 5.0 26.2 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 15:43:10 2025

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