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Chlorine in PDB 7g3p: Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm, PDB code: 7g3p was solved by M.Stihle, J.Benz, D.Hunziker, E.Pinard, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.81 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.842, 91.574, 119.916, 90, 90, 90
R / Rfree (%) 16.9 / 19.9

Other elements in 7g3p:

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm (pdb code 7g3p). 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-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm, PDB code: 7g3p:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7g3p

Go back to Chlorine Binding Sites List in 7g3p
Chlorine binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 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-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:20.0
occ:1.00
 CL2 A:YOI901 0.0 20.0 1.0
C1 A:YOI901 1.8 15.0 1.0
C3 A:YOI901 2.7 14.1 1.0
C27 A:YOI901 2.8 14.3 1.0
C4 A:YOI901 3.2 14.7 1.0
O A:LEU213 3.4 14.6 1.0
C A:LEU213 3.7 12.7 1.0
CZ A:PHE274 3.7 25.9 1.0
CH2 A:TRP260 3.8 16.7 1.0
CB A:LEU213 3.8 13.6 1.0
CB A:ALA217 3.9 15.2 1.0
CZ3 A:TRP260 3.9 17.6 1.0
C23 A:YOI901 4.0 13.6 1.0
C25 A:YOI901 4.0 15.6 1.0
N A:TYR214 4.1 12.3 1.0
CA A:TYR214 4.2 13.8 1.0
CE1 A:PHE274 4.2 28.9 1.0
CD1 A:TYR214 4.3 19.4 1.0
CA A:LEU213 4.3 12.8 1.0
CE2 A:PHE274 4.5 27.0 1.0
C24 A:YOI901 4.6 17.4 1.0
C5 A:YOI901 4.6 14.9 1.0
CB A:TYR214 4.9 14.8 1.0
CG A:LEU213 5.0 13.4 1.0

Chlorine binding site 2 out of 2 in 7g3p

Go back to Chlorine Binding Sites List in 7g3p
Chlorine binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 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-[(4,6-Dichloro- 2,3-Dihydro-1H-Inden-2-Yl)Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles C1(Cl) C2C[C@@H](NC3NCC(CN3)C(=O)N3CCC43COC4)CC2CC(Cl)C1 with IC50=0.0133598 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:19.7
occ:1.00
 CL26 A:YOI901 0.0 19.7 1.0
C25 A:YOI901 1.7 15.6 1.0
C24 A:YOI901 2.7 17.4 1.0
C27 A:YOI901 2.7 14.3 1.0
CG2 A:ILE167 3.8 14.8 1.0
CB A:LEU216 3.8 13.3 1.0
C23 A:YOI901 3.9 13.6 1.0
C1 A:YOI901 4.0 15.0 1.0
CD1 A:ILE167 4.0 15.4 1.0
CE2 A:PHE273 4.2 17.5 1.0
CE A:MET512 4.4 15.8 1.0
C A:LEU216 4.4 12.3 1.0
C3 A:YOI901 4.4 14.1 1.0
N A:ALA217 4.5 11.7 1.0
CD2 A:PHE273 4.5 16.6 1.0
CD1 A:LEU216 4.6 19.2 1.0
O A:LEU216 4.6 13.9 1.0
CB A:ILE167 4.6 14.4 1.0
SD A:MET512 4.6 15.8 1.0
CG1 A:ILE167 4.7 13.7 1.0
CA A:ALA217 4.8 13.8 1.0
CA A:LEU216 4.8 13.1 1.0
CG A:LEU216 4.8 14.5 1.0
O A:LEU213 5.0 14.6 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: Sun Jul 13 01:05:09 2025

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