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Chlorine in PDB 7g4r: Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm, PDB code: 7g4r 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) 46.48 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.497, 92.96, 120.809, 90, 90, 90
R / Rfree (%) 18.3 / 22

Other elements in 7g4r:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
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 (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm (pdb code 7g4r). 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 (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm, PDB code: 7g4r:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7g4r

Go back to Chlorine Binding Sites List in 7g4r
Chlorine binding site 1 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 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 (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:33.3
occ:1.00
 CL34 A:XF9901 0.0 33.3 1.0
C32 A:XF9901 1.7 26.4 1.0
C33 A:XF9901 2.7 28.9 1.0
C31 A:XF9901 2.7 26.0 1.0
CZ A:PHE274 3.5 39.5 1.0
CD1 A:TYR214 3.7 26.2 1.0
N A:TYR214 3.8 21.8 1.0
CA A:TYR214 3.8 25.6 1.0
C A:LEU213 3.9 24.2 1.0
CB A:LEU213 3.9 25.1 1.0
C30 A:XF9901 4.0 27.1 1.0
C28 A:XF9901 4.0 27.9 1.0
O A:LEU213 4.0 23.7 1.0
CH2 A:TRP260 4.1 31.1 1.0
CB A:TYR214 4.1 24.2 1.0
CE2 A:PHE274 4.1 41.0 1.0
CE1 A:PHE274 4.3 37.4 1.0
CG A:TYR214 4.4 27.3 1.0
C29 A:XF9901 4.5 27.9 1.0
CA A:LEU213 4.6 26.7 1.0
CZ3 A:TRP260 4.6 31.7 1.0
CE1 A:TYR214 4.7 28.8 1.0
CZ3 A:TRP254 4.8 35.5 1.0
CB A:ALA217 4.9 23.2 1.0

Chlorine binding site 2 out of 4 in 7g4r

Go back to Chlorine Binding Sites List in 7g4r
Chlorine binding site 2 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 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 (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl905

b:57.6
occ:1.00
 O A:HOH1169 3.0 35.8 1.0
NH1 A:ARG746 3.1 25.0 0.5
NH2 A:ARG746 3.5 29.9 0.5
O A:HOH1361 3.5 38.1 1.0
N A:GLU749 3.5 37.8 1.0
CZ A:ARG746 3.8 25.3 0.5
NH2 A:ARG746 3.8 30.2 0.5
CA A:THR748 3.9 31.9 1.0
CE1 A:PHE625 4.0 34.4 1.0
CB A:GLU749 4.1 46.2 1.0
C A:THR748 4.2 34.4 1.0
CZ A:PHE625 4.3 33.1 1.0
CB A:THR748 4.3 36.6 1.0
CE2 A:TYR605 4.4 24.3 1.0
CA A:GLU749 4.4 41.1 1.0
CD2 A:TYR605 4.6 28.1 1.0
CG2 A:THR748 4.7 30.9 1.0
O A:ASP747 4.8 27.8 1.0
O A:ARG606 5.0 37.0 1.0

Chlorine binding site 3 out of 4 in 7g4r

Go back to Chlorine Binding Sites List in 7g4r
Chlorine binding site 3 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 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 (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl906

b:75.2
occ:1.00
 O A:HOH1280 2.8 40.1 1.0
O A:HOH1355 3.1 35.8 1.0
NH2 A:ARG174 3.3 32.8 1.0
OG A:SER176 3.7 31.3 1.0
CB A:SER176 3.8 31.2 1.0
NE A:ARG174 3.9 27.7 1.0
CG2 A:ILE862 4.1 64.5 1.0
CZ A:ARG174 4.1 28.9 1.0
C A:ILE862 4.3 85.9 1.0
CA A:ILE862 4.3 83.1 1.0
CB A:ASN481 4.5 31.8 1.0
O A:ASN481 4.5 23.4 1.0
CB A:ILE862 4.7 71.7 1.0
CD1 A:ILE862 4.7 46.6 1.0
C A:ASN481 4.7 27.2 1.0
CG1 A:ILE862 4.9 60.9 1.0
O A:HOH1049 5.0 44.0 1.0

Chlorine binding site 4 out of 4 in 7g4r

Go back to Chlorine Binding Sites List in 7g4r
Chlorine binding site 4 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 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 (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl907

b:59.1
occ:1.00
 ND2 A:ASN801 3.0 30.3 1.0
NH2 A:ARG710 3.0 38.2 1.0
O A:HOH1092 3.3 32.8 1.0
O A:HOH1064 3.4 36.5 1.0
CB A:ASN801 3.9 28.2 1.0
CG A:ASN801 3.9 36.7 1.0
CD A:ARG710 4.0 35.6 1.0
CB A:ALA707 4.1 31.1 1.0
CZ A:ARG710 4.2 34.5 1.0
N A:ASN801 4.3 31.6 1.0
CA A:ALA707 4.3 31.9 1.0
NE A:ARG710 4.6 35.6 1.0
CA A:ASN801 4.7 32.5 1.0
O A:ALA707 4.8 29.4 1.0
OG A:SER807 4.8 30.1 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 16:57:04 2025

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