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Chlorine in PDB 7g3h: Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm, PDB code: 7g3h 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) 72.40 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.504, 91.217, 119.043, 90, 90, 90
R / Rfree (%) 16.9 / 19.8

Other elements in 7g3h:

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm (pdb code 7g3h). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm, PDB code: 7g3h:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7g3h

Go back to Chlorine Binding Sites List in 7g3h
Chlorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 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-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl904

b:44.8
occ:1.00
 N A:ASN230 3.3 31.2 1.0
NH1 A:ARG391 3.4 27.4 1.0
CA A:GLY229 3.6 23.6 1.0
N A:SER231 3.7 31.9 1.0
C A:GLY229 3.9 26.7 1.0
OG A:SER231 4.1 40.9 0.5
O A:SER231 4.1 29.5 1.0
CG1 A:VAL385 4.2 29.4 1.0
CA A:ASN230 4.3 33.2 1.0
CE A:LYS208 4.3 27.3 1.0
CD1 A:LEU389 4.4 31.4 1.0
CZ A:ARG391 4.5 26.4 1.0
C A:ASN230 4.5 34.2 1.0
CG A:LYS208 4.5 21.9 1.0
CB A:ASN230 4.6 35.2 1.0
CD2 A:LEU389 4.6 32.7 1.0
CB A:SER231 4.6 36.6 0.5
CA A:SER231 4.6 32.8 0.5
CA A:SER231 4.6 31.6 0.5
CB A:SER231 4.6 34.0 0.5
NH2 A:ARG391 4.7 27.9 1.0
CG A:LEU389 4.8 27.7 1.0
C A:SER231 4.8 30.5 1.0
N A:GLY229 4.9 20.0 1.0

Chlorine binding site 2 out of 3 in 7g3h

Go back to Chlorine Binding Sites List in 7g3h
Chlorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 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-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl910

b:24.5
occ:0.50
 CL1 A:XJ6910 0.0 24.5 0.5
CL1 A:XJ6910 0.0 24.6 0.5
C2 A:XJ6910 1.7 19.5 0.5
C2 A:XJ6910 1.8 19.4 0.5
C3 A:XJ6910 2.7 18.4 0.5
C3 A:XJ6910 2.7 18.4 0.5
C7 A:XJ6910 2.7 19.0 0.5
C7 A:XJ6910 2.7 19.0 0.5
CG2 A:ILE167 3.7 19.4 1.0
CD1 A:ILE167 3.9 21.6 1.0
C4 A:XJ6910 4.0 18.0 0.5
C4 A:XJ6910 4.0 18.0 0.5
CB A:LEU216 4.0 16.9 1.0
C6 A:XJ6910 4.0 17.7 0.5
C6 A:XJ6910 4.0 17.7 0.5
CE A:MET512 4.2 18.9 1.0
CE2 A:PHE273 4.2 22.8 1.0
SD A:MET512 4.3 19.8 1.0
CB A:ILE167 4.4 18.6 1.0
CG1 A:ILE167 4.4 19.0 1.0
C A:LEU216 4.5 15.7 1.0
C5 A:XJ6910 4.5 17.7 0.5
C5 A:XJ6910 4.5 17.7 0.5
CD2 A:PHE273 4.5 20.4 1.0
O A:LEU216 4.6 16.4 1.0
N A:ALA217 4.6 15.4 1.0
CD1 A:LEU216 4.8 23.6 1.0
CA A:LEU216 4.9 16.1 1.0
CA A:ALA217 4.9 16.6 1.0
CG A:LEU216 4.9 20.5 1.0

Chlorine binding site 3 out of 3 in 7g3h

Go back to Chlorine Binding Sites List in 7g3h
Chlorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Rat Autotaxin in Complex with [2-[[(2R)-5-Chloro- 2,3-Dihydro-1H-Inden-2-Yl]Amino]Pyrimidin-5-Yl]-(6-Oxa-1- Azaspiro[3.3]Heptan-1-Yl)Methanone, I.E. Smiles CLC1CCC2C(C1) C[C@@H](C2)NC1NCC(CN1)C(=O)N1CCC21COC2 with IC50=0.0678127 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl910

b:24.6
occ:0.50
 CL1 A:XJ6910 0.0 24.6 0.5
CL1 A:XJ6910 0.0 24.5 0.5
C2 A:XJ6910 1.7 19.5 0.5
C2 A:XJ6910 1.7 19.4 0.5
C3 A:XJ6910 2.7 18.4 0.5
C3 A:XJ6910 2.7 18.4 0.5
C7 A:XJ6910 2.7 19.0 0.5
C7 A:XJ6910 2.7 19.0 0.5
CG2 A:ILE167 3.7 19.4 1.0
CD1 A:ILE167 3.9 21.6 1.0
C4 A:XJ6910 4.0 18.0 0.5
C4 A:XJ6910 4.0 18.0 0.5
CB A:LEU216 4.0 16.9 1.0
C6 A:XJ6910 4.0 17.7 0.5
C6 A:XJ6910 4.0 17.7 0.5
CE A:MET512 4.2 18.9 1.0
CE2 A:PHE273 4.2 22.8 1.0
SD A:MET512 4.3 19.8 1.0
CB A:ILE167 4.4 18.6 1.0
CG1 A:ILE167 4.4 19.0 1.0
C A:LEU216 4.5 15.7 1.0
C5 A:XJ6910 4.5 17.7 0.5
C5 A:XJ6910 4.5 17.7 0.5
CD2 A:PHE273 4.5 20.4 1.0
O A:LEU216 4.6 16.4 1.0
N A:ALA217 4.6 15.4 1.0
CD1 A:LEU216 4.8 23.6 1.0
CA A:LEU216 4.9 16.1 1.0
CA A:ALA217 4.9 16.6 1.0
CG A:LEU216 4.9 20.5 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 01:04:35 2025

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