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Chlorine in PDB 7g7g: Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm, PDB code: 7g7g was solved by M.Stihle, J.Benz, D.Hunziker, E.Martin-Rainer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.61 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.756, 91.705, 119.371, 90, 90, 90
R / Rfree (%) 18.6 / 20.9

Other elements in 7g7g:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm (pdb code 7g7g). 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 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm, PDB code: 7g7g:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7g7g

Go back to Chlorine Binding Sites List in 7g7g
Chlorine binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 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 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl905

b:25.6
occ:1.00
 CL7 A:XI8905 0.0 25.6 1.0
C5 A:XI8905 1.7 24.3 1.0
C6 A:XI8905 2.7 22.4 1.0
C4 A:XI8905 2.7 23.4 1.0
CL8 A:XI8905 3.1 27.3 1.0
CD2 A:PHE210 3.6 25.6 1.0
CB A:LEU213 3.7 16.5 1.0
CZ3 A:TRP254 3.7 21.0 1.0
CE1 A:PHE274 3.8 21.2 1.0
CH2 A:TRP254 3.8 21.5 1.0
O A:PHE210 3.9 16.1 1.0
N A:TYR214 3.9 14.3 1.0
C1 A:XI8905 4.0 21.1 1.0
C3 A:XI8905 4.0 22.7 1.0
CE2 A:PHE210 4.1 25.3 1.0
CB A:TYR214 4.2 15.4 1.0
CA A:PHE210 4.2 16.9 1.0
C A:LEU213 4.2 15.0 1.0
CG A:PHE210 4.3 19.8 1.0
CA A:TYR214 4.4 13.6 1.0
C2 A:XI8905 4.5 22.8 1.0
CA A:LEU213 4.5 15.7 1.0
CB A:PHE210 4.5 18.5 1.0
C A:PHE210 4.5 15.8 1.0
CD1 A:PHE274 4.5 22.0 1.0
CD1 A:LEU213 4.6 21.1 1.0
CZ A:PHE274 4.7 23.1 1.0
CD1 A:TYR214 4.8 16.1 1.0
CG A:LEU213 4.8 17.7 1.0
CG A:TYR214 4.9 15.5 1.0
O A:LEU213 4.9 15.3 1.0
CE3 A:TRP254 4.9 21.3 1.0
O A:THR209 5.0 16.2 1.0

Chlorine binding site 2 out of 2 in 7g7g

Go back to Chlorine Binding Sites List in 7g7g
Chlorine binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 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 2-[7-(1- Acetylpiperidin-4-Yl)-4-Oxopyrido[1,2-A]Pyrimidin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]-N-Methylacetamide, I.E. Smiles C1(Ccc(C(C1) Cl)Cl)Cn(C(=O)CC1=Cn=C2C=Cc(=CN2C1=O)C1CCN(CC1)C(=O)C)C with IC50=0.798931 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl905

b:27.3
occ:1.00
 CL8 A:XI8905 0.0 27.3 1.0
C4 A:XI8905 1.7 23.4 1.0
C3 A:XI8905 2.6 22.7 1.0
C5 A:XI8905 2.7 24.3 1.0
CL7 A:XI8905 3.1 25.6 1.0
O A:LEU213 3.5 15.3 1.0
O A:HOH1457 3.7 26.6 1.0
C A:LEU213 3.7 15.0 1.0
CD1 A:TYR214 3.9 16.1 1.0
C2 A:XI8905 3.9 22.8 1.0
CE1 A:PHE274 3.9 21.2 1.0
N A:TYR214 4.0 14.3 1.0
CA A:TYR214 4.0 13.6 1.0
C6 A:XI8905 4.0 22.4 1.0
CH2 A:TRP260 4.0 19.7 1.0
CB A:LEU213 4.1 16.5 1.0
CB A:ALA217 4.1 18.7 1.0
CZ3 A:TRP260 4.2 18.7 1.0
CZ A:PHE274 4.2 23.1 1.0
C1 A:XI8905 4.4 21.1 1.0
CB A:TYR214 4.5 15.4 1.0
CA A:LEU213 4.5 15.7 1.0
CD1 A:PHE274 4.6 22.0 1.0
CG A:TYR214 4.7 15.5 1.0
O A:HOH1483 4.8 30.1 1.0
CE1 A:TYR214 4.8 16.8 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 17:09:54 2025

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