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Chlorine 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:

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

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 2 in 7g54

Go back to Chlorine Binding Sites List in 7g54
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl901

b:23.8
occ:1.00
 CL08 A:Y8U901 0.0 23.8 1.0
C03 A:Y8U901 1.7 21.7 1.0
C04 A:Y8U901 2.7 22.4 1.0
C02 A:Y8U901 2.7 21.6 1.0
SD A:MET512 3.6 28.4 1.0
CG1 A:VAL356 3.7 19.0 1.0
CG2 A:ILE167 3.8 18.7 1.0
CE A:MET512 3.8 25.1 1.0
CD2 A:LEU216 3.8 18.6 1.0
C05 A:Y8U901 4.0 22.7 1.0
C01 A:Y8U901 4.0 21.3 1.0
CB A:LEU216 4.1 18.8 1.0
CD1 A:ILE167 4.2 20.9 1.0
CG A:LEU216 4.3 19.4 1.0
CD1 A:LEU216 4.5 18.9 1.0
C06 A:Y8U901 4.6 22.6 1.0
CG1 A:ILE167 4.6 19.7 1.0
CD1 A:LEU508 4.6 27.6 1.0
CG2 A:ILE354 4.7 20.9 1.0
CB A:VAL356 4.7 19.1 1.0
O A:LEU216 4.8 18.9 1.0
CB A:ILE167 4.8 20.0 1.0
CG2 A:VAL356 4.9 19.1 1.0
CA A:LEU216 5.0 18.7 1.0
C A:LEU216 5.0 19.3 1.0

Chlorine binding site 2 out of 2 in 7g54

Go back to Chlorine Binding Sites List in 7g54
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl905

b:35.2
occ:1.00
 N A:ASN230 3.6 27.6 1.0
NZ A:LYS208 3.6 31.1 1.0
N A:SER231 3.8 27.5 1.0
NH1 A:ARG391 3.8 25.4 1.0
CA A:GLY229 4.1 24.7 1.0
O A:HOH1208 4.1 29.8 1.0
C A:GLY229 4.3 25.0 1.0
CG1 A:VAL385 4.3 27.5 1.0
CB A:SER231 4.4 27.5 1.0
O A:SER231 4.4 28.6 1.0
CA A:ASN230 4.4 27.1 1.0
CB A:ASN230 4.5 27.1 1.0
C A:ASN230 4.6 27.1 1.0
CD2 A:LEU389 4.6 24.7 1.0
CA A:SER231 4.6 27.7 1.0
CG A:LYS208 4.6 25.7 1.0
CZ A:ARG391 4.8 25.0 1.0
CE A:LYS208 5.0 29.6 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 16:59:03 2025

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