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Chlorine in PDB 7g57: Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 Microm, PDB code: 7g57 was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.43 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.61, 92.951, 121.087, 90, 90, 90
R / Rfree (%) 20.7 / 25.1

Other elements in 7g57:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 Microm also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 Microm (pdb code 7g57). 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 (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 Microm, PDB code: 7g57:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7g57

Go back to Chlorine Binding Sites List in 7g57
Chlorine binding site 1 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 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 (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl902

b:56.4
occ:1.00
 CL30 A:YGB902 0.0 56.4 1.0
C26 A:YGB902 1.7 48.7 1.0
C27 A:YGB902 2.7 45.7 1.0
C25 A:YGB902 2.7 48.4 1.0
CD2 A:LEU216 3.4 32.2 0.3
CG A:LEU216 3.7 32.3 0.3
CG2 A:ILE167 3.9 31.2 1.0
CB A:LEU216 3.9 32.1 0.3
C28 A:YGB902 3.9 46.6 1.0
C24 A:YGB902 3.9 50.1 1.0
CB A:LEU216 4.0 33.9 0.7
CD1 A:LEU216 4.3 34.9 0.7
C29 A:YGB902 4.4 48.8 1.0
CB A:SER169 4.5 40.6 1.0
O A:LEU213 4.5 27.3 1.0
CD2 A:LEU213 4.5 30.4 1.0
CG A:LEU216 4.7 34.9 0.7
OG A:SER169 4.8 43.4 1.0
CE2 A:PHE273 4.8 42.3 1.0
CD2 A:PHE273 4.9 43.5 1.0
N A:ALA217 4.9 30.9 1.0
CB A:ILE167 4.9 32.7 1.0
CD1 A:ILE167 5.0 33.2 1.0

Chlorine binding site 2 out of 4 in 7g57

Go back to Chlorine Binding Sites List in 7g57
Chlorine binding site 2 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 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 (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl902

b:48.2
occ:1.00
 CL31 A:YGB902 0.0 48.2 1.0
C28 A:YGB902 1.7 46.6 1.0
C27 A:YGB902 2.7 45.7 1.0
C29 A:YGB902 2.7 48.8 1.0
O A:LEU213 3.7 27.3 1.0
CH2 A:TRP260 3.8 40.2 1.0
C A:LEU213 3.9 27.5 1.0
C26 A:YGB902 3.9 48.7 1.0
CZ3 A:TRP260 4.0 40.5 1.0
CB A:LEU213 4.0 29.0 1.0
C24 A:YGB902 4.0 50.1 1.0
CB A:ALA217 4.0 28.6 1.0
N A:TYR214 4.1 28.4 1.0
CA A:TYR214 4.2 28.9 1.0
CD1 A:TYR214 4.3 30.6 1.0
C25 A:YGB902 4.5 48.4 1.0
CA A:LEU213 4.5 28.8 1.0
CB A:TYR214 4.8 30.5 1.0

Chlorine binding site 3 out of 4 in 7g57

Go back to Chlorine Binding Sites List in 7g57
Chlorine binding site 3 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 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 (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl906

b:50.5
occ:1.00
 N A:ASN230 3.6 37.5 1.0
NZ A:LYS208 3.6 50.5 1.0
N A:SER231 3.8 36.0 1.0
NH1 A:ARG391 3.8 37.2 1.0
CA A:GLY229 3.9 32.6 1.0
O A:SER231 4.2 42.4 1.0
CG1 A:VAL385 4.2 43.3 1.0
C A:GLY229 4.2 34.5 1.0
CA A:ASN230 4.4 36.1 1.0
CB A:SER231 4.4 42.2 1.0
CB A:ASN230 4.4 35.0 1.0
C A:ASN230 4.6 37.0 1.0
CA A:SER231 4.6 38.5 1.0
CD1 A:LEU389 4.7 32.4 1.0
CG A:LYS208 4.8 42.6 1.0
CZ A:ARG391 4.8 38.8 1.0
CE A:LYS208 4.8 46.8 1.0
NH2 A:ARG391 4.8 40.3 1.0
C A:SER231 4.9 38.8 1.0
CD2 A:LEU389 5.0 35.0 1.0
CD A:LYS208 5.0 46.5 1.0
CG A:LEU389 5.0 33.1 1.0

Chlorine binding site 4 out of 4 in 7g57

Go back to Chlorine Binding Sites List in 7g57
Chlorine binding site 4 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 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 (3,5- Dichlorophenyl)Methyl Rac-(3AR,6AS)-5-(1H-Triazol-5- Ylmethylcarbamoyl)-3,3A,4,5,6,6A-Hexahydro-1H-Cyclopenta[C]Pyrrole-2- Carboxylate, I.E. Smiles [C@H]12CN(C[C@H]1C[C@@H](C2)C(=O) NCC1=Cn=NN1)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.326297 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl907

b:68.0
occ:1.00
 NH2 A:ARG710 3.0 38.6 1.0
ND2 A:ASN801 3.1 39.7 1.0
O A:HOH1167 3.2 44.2 1.0
CD A:ARG710 3.7 38.2 1.0
O A:HOH1008 3.7 51.0 1.0
CB A:ASN801 4.0 37.7 1.0
CG A:ASN801 4.0 40.7 1.0
CZ A:ARG710 4.1 40.1 1.0
CB A:ALA707 4.1 35.8 1.0
CA A:ALA707 4.3 35.0 1.0
NE A:ARG710 4.3 39.7 1.0
N A:ASN801 4.7 38.8 1.0
O A:ALA707 4.7 34.4 1.0
CG A:ARG710 4.8 38.0 1.0
OG A:SER807 4.9 38.9 1.0
CA A:ASN801 5.0 37.2 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 17:01:13 2025

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