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Zinc 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:

Chlorine (Cl) 4 atoms
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7g57

Go back to Zinc Binding Sites List in 7g57
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn901

b:36.8
occ:1.00
 OG1 A:THR209 1.9 35.2 1.0
OD1 A:ASP171 1.9 33.7 1.0
OD2 A:ASP358 2.1 31.0 1.0
NE2 A:HIS359 2.1 30.6 1.0
CG A:ASP171 2.6 32.9 1.0
OD2 A:ASP171 2.7 33.1 1.0
CB A:THR209 2.9 33.8 1.0
CE1 A:HIS359 2.9 30.3 1.0
CG A:ASP358 3.0 31.1 1.0
CD2 A:HIS359 3.0 29.8 1.0
OD1 A:ASP358 3.3 29.9 1.0
CG2 A:THR209 3.3 35.2 1.0
CA A:THR209 3.3 33.4 1.0
N A:THR209 3.8 33.5 1.0
ND1 A:HIS359 4.0 29.5 1.0
CB A:ASP171 4.0 32.1 1.0
CG A:HIS359 4.0 30.1 1.0
O A:HOH1015 4.1 45.1 1.0
O2 A:SO4903 4.1 77.5 1.0
N A:GLY172 4.2 31.4 1.0
CB A:ASP358 4.3 28.6 1.0
CG A:ASP311 4.4 33.3 1.0
OD1 A:ASP311 4.4 32.9 1.0
CE1 A:HIS474 4.4 30.1 1.0
CA A:ASP171 4.4 32.4 1.0
OD2 A:ASP311 4.6 32.9 1.0
C A:LYS208 4.6 34.7 1.0
NE2 A:HIS474 4.6 30.9 1.0
ZN A:ZN904 4.6 34.5 1.0
C A:THR209 4.7 31.8 1.0
C A:ASP171 4.7 32.7 1.0
CB A:ASP311 4.8 33.0 1.0

Zinc binding site 2 out of 2 in 7g57

Go back to Zinc Binding Sites List in 7g57
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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:Zn904

b:34.5
occ:1.00
 O2 A:SO4903 1.9 77.5 1.0
NE2 A:HIS474 2.0 30.9 1.0
NE2 A:HIS315 2.1 34.3 1.0
OD2 A:ASP311 2.1 32.9 1.0
OD1 A:ASP311 2.4 32.9 1.0
S A:SO4903 2.5 80.0 1.0
O3 A:SO4903 2.6 80.0 1.0
CG A:ASP311 2.6 33.3 1.0
O4 A:SO4903 3.0 80.0 1.0
CD2 A:HIS315 3.0 32.6 1.0
CE1 A:HIS474 3.0 30.1 1.0
CD2 A:HIS474 3.0 30.3 1.0
CE1 A:HIS315 3.1 34.1 1.0
O1 A:SO4903 3.9 80.0 1.0
CB A:ASP311 4.1 33.0 1.0
N16 A:YGB902 4.1 60.8 1.0
ND1 A:HIS474 4.1 30.8 1.0
O A:HOH1015 4.1 45.1 1.0
CG A:HIS315 4.2 33.2 1.0
CG A:HIS474 4.2 30.3 1.0
ND1 A:HIS315 4.2 33.6 1.0
CE1 A:HIS359 4.2 30.3 1.0
N17 A:YGB902 4.3 57.9 1.0
NE2 A:HIS359 4.5 30.6 1.0
OG1 A:THR209 4.5 35.2 1.0
CE A:MET361 4.6 34.1 1.0
ZN A:ZN901 4.6 36.8 1.0
OD1 A:ASP171 4.8 33.7 1.0
O A:ASP311 4.8 31.4 1.0
C A:ASP311 5.0 33.9 1.0
CA A:ASP311 5.0 34.2 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: Sun Feb 9 00:28:26 2025

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