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Chlorine in PDB 7g4d: Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm, PDB code: 7g4d 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) 46.23 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.151, 92.454, 120.601, 90, 90, 90
R / Rfree (%) 22.6 / 28.2

Other elements in 7g4d:

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Calcium (Ca) 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 Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm (pdb code 7g4d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm, PDB code: 7g4d:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7g4d

Go back to Chlorine Binding Sites List in 7g4d
Chlorine binding site 1 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 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 Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl904

b:58.2
occ:1.00
 NH1 A:ARG746 2.8 40.7 1.0
O A:HOH1131 2.9 47.6 1.0
NH2 A:ARG746 3.5 39.2 1.0
CZ A:ARG746 3.6 41.0 1.0
N A:GLU749 3.6 36.2 1.0
CA A:THR748 3.8 32.7 1.0
CE1 A:PHE625 3.9 34.2 1.0
CB A:THR748 4.0 33.6 1.0
CZ A:PHE625 4.2 33.6 1.0
C A:THR748 4.2 34.0 1.0
CG2 A:THR748 4.3 33.2 1.0
CE2 A:TYR605 4.4 27.2 1.0
CB A:GLU749 4.5 46.5 1.0
CD2 A:TYR605 4.5 28.3 1.0
CA A:GLU749 4.7 39.7 1.0
O A:ASP747 4.8 30.7 1.0
NE A:ARG746 4.9 42.0 1.0
O A:ARG606 5.0 30.9 1.0
OG1 A:THR607 5.0 33.8 1.0

Chlorine binding site 2 out of 4 in 7g4d

Go back to Chlorine Binding Sites List in 7g4d
Chlorine binding site 2 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 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 Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl905

b:73.5
occ:1.00
 N A:ASN230 3.2 41.2 1.0
NH1 A:ARG391 3.5 42.2 1.0
NZ A:LYS208 3.7 39.6 1.0
CA A:GLY229 3.7 33.9 1.0
N A:SER231 3.9 48.5 1.0
C A:GLY229 3.9 36.9 1.0
CA A:ASN230 4.1 45.1 1.0
CB A:ASN230 4.2 46.4 1.0
CG A:LYS208 4.4 29.8 1.0
CG1 A:VAL385 4.4 35.7 1.0
CD2 A:LEU389 4.4 39.5 1.0
C A:ASN230 4.4 47.9 1.0
O A:SER231 4.5 47.3 1.0
CZ A:ARG391 4.5 41.0 1.0
NH2 A:ARG391 4.6 41.5 1.0
CB A:SER231 4.7 47.6 1.0
CD1 A:LEU389 4.8 42.1 1.0
CD A:LYS208 4.8 33.1 1.0
CA A:SER231 4.8 46.0 1.0
CG A:LEU389 4.8 40.2 1.0
CE A:LYS208 4.9 37.0 1.0

Chlorine binding site 3 out of 4 in 7g4d

Go back to Chlorine Binding Sites List in 7g4d
Chlorine binding site 3 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 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 Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl906

b:75.0
occ:1.00
 NH2 A:ARG174 2.9 25.5 1.0
O A:HOH1253 3.0 33.2 1.0
OG A:SER176 3.4 28.4 1.0
NE A:ARG174 3.6 24.2 1.0
CZ A:ARG174 3.7 24.2 1.0
CB A:SER176 3.8 25.5 1.0
N A:GLY863 4.0 80.0 1.0
CG2 A:ILE862 4.2 80.0 1.0
O A:ASN481 4.3 30.1 1.0
C A:ASN481 4.5 30.5 1.0
CB A:ASN481 4.6 35.2 1.0
CA A:GLY863 4.7 80.0 1.0
CA A:SER482 4.7 26.9 1.0
N A:SER482 4.8 27.1 1.0
CA A:ILE862 4.8 80.0 1.0
C A:ILE862 4.9 80.0 1.0
CD1 A:ILE862 5.0 80.0 1.0
CD A:ARG174 5.0 24.3 1.0
CA A:SER176 5.0 26.2 1.0

Chlorine binding site 4 out of 4 in 7g4d

Go back to Chlorine Binding Sites List in 7g4d
Chlorine binding site 4 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Rat Autotaxin in Complex with Rac-(E)-1-[Rac-(1R, 2S,6R,7S)-9-(1H-Benzotriazole-5-Carbonyl)-4,9-Diazatricyclo[5.3.0.02, 6]Decan-4-Yl]-3-[4-(Trifluoromethoxy)Phenyl]Prop-2-En-1-One, 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)/C=C/C1CCC(CC1)Oc(F)(F)F with IC50=0.00827722 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl907

b:66.4
occ:1.00
 NH2 A:ARG710 2.9 34.7 1.0
ND2 A:ASN801 2.9 32.1 1.0
O A:HOH1129 2.9 33.2 1.0
CD A:ARG710 3.9 31.8 1.0
CG A:ASN801 3.9 32.6 1.0
CB A:ALA707 3.9 26.2 1.0
CB A:ASN801 4.0 30.1 1.0
CZ A:ARG710 4.0 34.6 1.0
CA A:ALA707 4.2 25.0 1.0
NE A:ARG710 4.4 33.7 1.0
N A:ASN801 4.5 32.0 1.0
O A:ALA707 4.6 25.2 1.0
C A:ALA707 4.9 25.1 1.0
CA A:ASN801 4.9 30.9 1.0
OG A:SER807 4.9 29.4 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 16:54:58 2025

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