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Zinc in PDB 7g54: Crystal Structure of Rat Autotaxin in Complex with Tert-Butyl (4AR)-9- (4-Chloro-2-Fluorophenyl)-5,11-Dioxo-2,4,4A,6-Tetrahydro-1H- Pyrazino[2,1-C][1,4]Benzodiazepine-3-Carboxylate, I.E. Smiles C1CC(Cc(C1C1CC2C(CC1)Nc(=O)[C@@H]1N(C2=O)Ccn(C1)C(=O)Oc(C)(C)C)F)Cl with IC50=0.506839 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Tert-Butyl (4AR)-9- (4-Chloro-2-Fluorophenyl)-5,11-Dioxo-2,4,4A,6-Tetrahydro-1H- Pyrazino[2,1-C][1,4]Benzodiazepine-3-Carboxylate, I.E. Smiles C1CC(Cc(C1C1CC2C(CC1)Nc(=O)[C@@H]1N(C2=O)Ccn(C1)C(=O)Oc(C)(C)C)F)Cl with IC50=0.506839 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Tert-Butyl (4AR)-9- (4-Chloro-2-Fluorophenyl)-5,11-Dioxo-2,4,4A,6-Tetrahydro-1H- Pyrazino[2,1-C][1,4]Benzodiazepine-3-Carboxylate, I.E. Smiles C1CC(Cc(C1C1CC2C(CC1)Nc(=O)[C@@H]1N(C2=O)Ccn(C1)C(=O)Oc(C)(C)C)F)Cl with IC50=0.506839 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with Tert-Butyl (4AR)-9- (4-Chloro-2-Fluorophenyl)-5,11-Dioxo-2,4,4A,6-Tetrahydro-1H- Pyrazino[2,1-C][1,4]Benzodiazepine-3-Carboxylate, I.E. Smiles C1CC(Cc(C1C1CC2C(CC1)Nc(=O)[C@@H]1N(C2=O)Ccn(C1)C(=O)Oc(C)(C)C)F)Cl with IC50=0.506839 Microm, PDB code: 7g54 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) 43.49 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.077, 93.061, 121.586, 90, 90, 90
R / Rfree (%) 23.1 / 29.3

Other elements in 7g54:

The structure of Crystal Structure of Rat Autotaxin in Complex with Tert-Butyl (4AR)-9- (4-Chloro-2-Fluorophenyl)-5,11-Dioxo-2,4,4A,6-Tetrahydro-1H- Pyrazino[2,1-C][1,4]Benzodiazepine-3-Carboxylate, I.E. Smiles C1CC(Cc(C1C1CC2C(CC1)Nc(=O)[C@@H]1N(C2=O)Ccn(C1)C(=O)Oc(C)(C)C)F)Cl with IC50=0.506839 Microm also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 1 atom
Fluorine (F) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin in Complex with Tert-Butyl (4AR)-9- (4-Chloro-2-Fluorophenyl)-5,11-Dioxo-2,4,4A,6-Tetrahydro-1H- Pyrazino[2,1-C][1,4]Benzodiazepine-3-Carboxylate, I.E. Smiles C1CC(Cc(C1C1CC2C(CC1)Nc(=O)[C@@H]1N(C2=O)Ccn(C1)C(=O)Oc(C)(C)C)F)Cl with IC50=0.506839 Microm (pdb code 7g54). 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 Tert-Butyl (4AR)-9- (4-Chloro-2-Fluorophenyl)-5,11-Dioxo-2,4,4A,6-Tetrahydro-1H- Pyrazino[2,1-C][1,4]Benzodiazepine-3-Carboxylate, I.E. Smiles C1CC(Cc(C1C1CC2C(CC1)Nc(=O)[C@@H]1N(C2=O)Ccn(C1)C(=O)Oc(C)(C)C)F)Cl with IC50=0.506839 Microm, PDB code: 7g54:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7g54

Go back to Zinc Binding Sites List in 7g54
Zinc binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with Tert-Butyl (4AR)-9- (4-Chloro-2-Fluorophenyl)-5,11-Dioxo-2,4,4A,6-Tetrahydro-1H- Pyrazino[2,1-C][1,4]Benzodiazepine-3-Carboxylate, I.E. Smiles C1CC(Cc(C1C1CC2C(CC1)Nc(=O)[C@@H]1N(C2=O)Ccn(C1)C(=O)Oc(C)(C)C)F)Cl with IC50=0.506839 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 Tert-Butyl (4AR)-9- (4-Chloro-2-Fluorophenyl)-5,11-Dioxo-2,4,4A,6-Tetrahydro-1H- Pyrazino[2,1-C][1,4]Benzodiazepine-3-Carboxylate, I.E. Smiles C1CC(Cc(C1C1CC2C(CC1)Nc(=O)[C@@H]1N(C2=O)Ccn(C1)C(=O)Oc(C)(C)C)F)Cl with IC50=0.506839 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:22.7
occ:1.00
 OG1 A:THR209 1.8 18.8 1.0
OD1 A:ASP171 1.9 20.2 1.0
OD2 A:ASP358 2.0 22.5 1.0
NE2 A:HIS359 2.1 20.1 1.0
CG A:ASP171 2.6 20.1 1.0
OD2 A:ASP171 2.7 19.2 1.0
CG A:ASP358 2.9 21.2 1.0
CB A:THR209 2.9 20.4 1.0
CD2 A:HIS359 2.9 20.2 1.0
CE1 A:HIS359 3.0 19.6 1.0
OD1 A:ASP358 3.1 21.1 1.0
CA A:THR209 3.3 21.4 1.0
CG2 A:THR209 3.3 20.2 1.0
N A:THR209 3.8 22.2 1.0
ND1 A:HIS359 4.0 20.0 1.0
CG A:HIS359 4.0 20.6 1.0
CB A:ASP171 4.0 19.5 1.0
N A:GLY172 4.1 18.0 1.0
OD2 A:ASP311 4.1 22.5 1.0
CB A:ASP358 4.2 19.5 1.0
CE1 A:HIS474 4.4 27.6 1.0
CA A:ASP171 4.4 19.1 1.0
CG A:ASP311 4.4 21.3 1.0
O A:HOH1222 4.5 31.7 1.0
ZN A:ZN903 4.5 23.2 1.0
C A:THR209 4.6 22.9 1.0
C A:ASP171 4.7 18.5 1.0
NE2 A:HIS474 4.7 27.4 1.0
C A:LYS208 4.7 22.0 1.0
CB A:ASP311 4.8 21.6 1.0
O A:HOH1264 4.8 30.4 1.0
OD1 A:ASP311 4.9 21.6 1.0
CA A:GLY172 5.0 17.8 1.0

Zinc binding site 2 out of 2 in 7g54

Go back to Zinc Binding Sites List in 7g54
Zinc binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with Tert-Butyl (4AR)-9- (4-Chloro-2-Fluorophenyl)-5,11-Dioxo-2,4,4A,6-Tetrahydro-1H- Pyrazino[2,1-C][1,4]Benzodiazepine-3-Carboxylate, I.E. Smiles C1CC(Cc(C1C1CC2C(CC1)Nc(=O)[C@@H]1N(C2=O)Ccn(C1)C(=O)Oc(C)(C)C)F)Cl with IC50=0.506839 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 Tert-Butyl (4AR)-9- (4-Chloro-2-Fluorophenyl)-5,11-Dioxo-2,4,4A,6-Tetrahydro-1H- Pyrazino[2,1-C][1,4]Benzodiazepine-3-Carboxylate, I.E. Smiles C1CC(Cc(C1C1CC2C(CC1)Nc(=O)[C@@H]1N(C2=O)Ccn(C1)C(=O)Oc(C)(C)C)F)Cl with IC50=0.506839 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:23.2
occ:1.00
 OD2 A:ASP311 1.9 22.5 1.0
O A:HOH1264 1.9 30.4 1.0
NE2 A:HIS474 2.0 27.4 1.0
NE2 A:HIS315 2.1 21.9 1.0
CG A:ASP311 2.6 21.3 1.0
OD1 A:ASP311 2.6 21.6 1.0
CE1 A:HIS474 2.9 27.6 1.0
CD2 A:HIS315 3.0 20.9 1.0
CE1 A:HIS315 3.1 21.5 1.0
CD2 A:HIS474 3.1 26.2 1.0
O A:HOH1222 3.7 31.7 1.0
ND1 A:HIS474 4.1 26.1 1.0
CE1 A:HIS359 4.1 19.6 1.0
CB A:ASP311 4.1 21.6 1.0
CG A:HIS315 4.2 21.1 1.0
ND1 A:HIS315 4.2 21.4 1.0
CG A:HIS474 4.2 26.4 1.0
OG1 A:THR209 4.2 18.8 1.0
NE2 A:HIS359 4.3 20.1 1.0
ZN A:ZN902 4.5 22.7 1.0
CE A:MET361 4.6 20.4 1.0
OD1 A:ASP171 4.6 20.2 1.0
O A:ASP311 4.8 20.8 1.0
CA A:ASP311 5.0 21.1 1.0
C A:ASP311 5.0 21.5 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 Feb 9 00:28:26 2025

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