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Chlorine in PDB 7g37: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[5-Chloro-4-(Cyclopropylmethoxy)Pyridine-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C(CN1)Cl)OCC1CC1 with IC50=0.190022 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[5-Chloro-4-(Cyclopropylmethoxy)Pyridine-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C(CN1)Cl)OCC1CC1 with IC50=0.190022 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[5-Chloro-4-(Cyclopropylmethoxy)Pyridine-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C(CN1)Cl)OCC1CC1 with IC50=0.190022 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[5-Chloro-4-(Cyclopropylmethoxy)Pyridine-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C(CN1)Cl)OCC1CC1 with IC50=0.190022 Microm, PDB code: 7g37 was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.92 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.307, 91.845, 120.385, 90, 90, 90
R / Rfree (%) 19.8 / 23.2

Other elements in 7g37:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[5-Chloro-4-(Cyclopropylmethoxy)Pyridine-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C(CN1)Cl)OCC1CC1 with IC50=0.190022 Microm also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[5-Chloro-4-(Cyclopropylmethoxy)Pyridine-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C(CN1)Cl)OCC1CC1 with IC50=0.190022 Microm (pdb code 7g37). 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[5-Chloro-4-(Cyclopropylmethoxy)Pyridine-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C(CN1)Cl)OCC1CC1 with IC50=0.190022 Microm, PDB code: 7g37:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7g37

Go back to Chlorine Binding Sites List in 7g37
Chlorine binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[5-Chloro-4-(Cyclopropylmethoxy)Pyridine-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C(CN1)Cl)OCC1CC1 with IC50=0.190022 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[5-Chloro-4-(Cyclopropylmethoxy)Pyridine-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C(CN1)Cl)OCC1CC1 with IC50=0.190022 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:38.5
occ:1.00
CL37 A:Y0Q901 0.0 38.5 1.0
C33 A:Y0Q901 1.7 31.9 1.0
C32 A:Y0Q901 2.6 33.0 1.0
C30 A:Y0Q901 2.8 31.2 1.0
O34 A:Y0Q901 2.9 35.6 1.0
C A:LEU213 3.6 19.6 1.0
N A:TYR214 3.6 19.4 1.0
CA A:TYR214 3.7 18.8 1.0
O A:LEU213 3.7 18.5 1.0
CD1 A:TYR214 3.7 21.3 1.0
CB A:LEU213 3.8 19.9 1.0
N31 A:Y0Q901 3.9 32.6 1.0
CB A:TYR214 4.0 21.1 1.0
C29 A:Y0Q901 4.0 31.0 1.0
C35 A:Y0Q901 4.3 37.0 1.0
CG A:TYR214 4.3 19.4 1.0
CA A:LEU213 4.3 19.8 1.0
CE1 A:PHE274 4.4 49.8 1.0
C27 A:Y0Q901 4.4 32.5 1.0
CH2 A:TRP260 4.4 26.0 1.0
CZ3 A:TRP254 4.5 26.9 1.0
C38 A:Y0Q901 4.6 37.4 1.0
CB A:ALA217 4.7 17.2 1.0
C36 A:Y0Q901 4.7 38.9 1.0
CE1 A:TYR214 4.8 22.0 1.0
CZ3 A:TRP260 5.0 25.1 1.0
O A:PHE210 5.0 23.0 1.0

Chlorine binding site 2 out of 2 in 7g37

Go back to Chlorine Binding Sites List in 7g37
Chlorine binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[5-Chloro-4-(Cyclopropylmethoxy)Pyridine-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C(CN1)Cl)OCC1CC1 with IC50=0.190022 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[5-Chloro-4-(Cyclopropylmethoxy)Pyridine-2- Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2) C(=O)C1CC(C(CN1)Cl)OCC1CC1 with IC50=0.190022 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl907

b:39.2
occ:1.00
N A:ASN230 3.2 29.9 1.0
NH1 A:ARG391 3.5 31.7 1.0
CA A:GLY229 3.5 24.1 1.0
N A:SER231 3.8 38.4 1.0
C A:GLY229 3.8 24.0 1.0
CE A:LYS208 4.0 28.7 1.0
O A:SER231 4.1 44.0 1.0
CA A:ASN230 4.2 32.1 1.0
CG A:LYS208 4.2 25.8 1.0
CB A:ASN230 4.3 30.2 1.0
CG1 A:VAL385 4.4 30.9 1.0
CD1 A:LEU389 4.4 32.5 1.0
C A:ASN230 4.5 36.2 1.0
CD A:LYS208 4.5 27.1 1.0
CB A:SER231 4.5 41.5 1.0
CZ A:ARG391 4.6 28.3 1.0
CA A:SER231 4.7 40.9 1.0
CD2 A:LEU389 4.7 33.7 1.0
NH2 A:ARG391 4.7 28.7 1.0
CG A:LEU389 4.8 29.9 1.0
NZ A:LYS208 4.8 33.5 1.0
C A:SER231 4.9 38.2 1.0
N A:GLY229 4.9 22.4 1.0
O A:HOH1030 4.9 35.7 1.0
O A:GLY229 5.0 28.5 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 01:03:44 2025

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