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Chlorine in PDB 7g3d: Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm, PDB code: 7g3d 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) 48.83 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.23, 91.79, 119.85, 90, 90, 90
R / Rfree (%) 17.7 / 21.8

Other elements in 7g3d:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm (pdb code 7g3d). 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 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm, PDB code: 7g3d:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7g3d

Go back to Chlorine Binding Sites List in 7g3d
Chlorine binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 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 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:27.6
occ:1.00
 CL8 A:XLL901 0.0 27.6 1.0
C7 A:XLL901 1.7 24.7 1.0
C9 A:XLL901 2.7 23.8 1.0
C6 A:XLL901 2.7 23.8 1.0
C10 A:XLL901 3.0 25.9 1.0
O A:LEU213 3.6 19.4 1.0
N11 A:XLL901 3.8 25.6 1.0
CB A:ALA217 3.8 21.1 1.0
C12 A:XLL901 3.9 23.8 1.0
CD2 A:PHE273 3.9 25.1 1.0
N A:ALA217 3.9 20.3 1.0
C5 A:XLL901 4.0 23.4 1.0
CA A:ALA217 4.1 21.1 1.0
CB A:LEU216 4.1 24.1 1.0
CE2 A:PHE273 4.1 25.0 1.0
C A:LEU216 4.4 21.4 1.0
C13 A:XLL901 4.5 23.9 1.0
C A:LEU213 4.6 17.4 1.0
CA A:LEU216 4.8 21.8 1.0
CZ3 A:TRP260 4.9 25.1 1.0
O A:LEU216 4.9 22.0 1.0
CA A:LEU213 5.0 18.6 1.0

Chlorine binding site 2 out of 2 in 7g3d

Go back to Chlorine Binding Sites List in 7g3d
Chlorine binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 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 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl908

b:67.5
occ:1.00
 CB A:CYS85 3.9 50.4 1.0
N A:CYS85 3.9 48.2 1.0
SG A:CYS85 3.9 55.6 1.0
C A:SER83 4.3 62.8 1.0
N A:SER84 4.3 56.0 1.0
CA A:SER83 4.3 68.0 1.0
NZ A:LYS80 4.4 68.7 1.0
CA A:CYS85 4.4 50.4 1.0
O A:CYS85 4.5 48.4 1.0
CD A:LYS80 4.6 66.2 1.0
O A:SER83 4.8 61.7 1.0
C A:CYS85 4.9 48.4 1.0
O A:CYS79 4.9 54.3 1.0
CA A:LYS80 4.9 63.5 1.0
C A:SER84 4.9 51.0 1.0
CE A:LYS80 4.9 67.8 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 16:51:14 2025

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