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Calcium in PDB 7g2k: Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm, PDB code: 7g2k 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) 45.78 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.892, 91.556, 119.073, 90, 90, 90
R / Rfree (%) 17.6 / 22.4

Other elements in 7g2k:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Fluorine (F) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm (pdb code 7g2k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm, PDB code: 7g2k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2k

Go back to Calcium Binding Sites List in 7g2k
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:35.0
occ:1.00
 OD1 A:ASP171 2.0 29.8 1.0
OG1 A:THR209 2.0 28.9 1.0
NE2 A:HIS359 2.2 22.3 1.0
OD2 A:ASP358 2.2 28.1 1.0
CG A:ASP171 2.6 28.2 1.0
OD2 A:ASP171 2.7 35.3 1.0
CB A:THR209 2.9 24.2 1.0
CG A:ASP358 3.1 24.9 1.0
CE1 A:HIS359 3.1 23.2 1.0
CD2 A:HIS359 3.1 21.9 1.0
CG2 A:THR209 3.2 27.8 1.0
OD1 A:ASP358 3.3 21.6 1.0
CA A:THR209 3.3 23.8 1.0
N A:THR209 3.9 22.9 1.0
CB A:ASP171 4.0 27.1 1.0
OD2 A:ASP311 4.0 26.1 1.0
N A:GLY172 4.1 23.1 1.0
ND1 A:HIS359 4.2 22.7 1.0
O3 A:SO4902 4.2 48.8 1.0
O1 A:SO4902 4.2 52.0 1.0
CG A:HIS359 4.2 22.0 1.0
CA A:ASP171 4.3 25.1 1.0
CB A:ASP358 4.4 23.0 1.0
CG A:ASP311 4.4 25.7 1.0
CE1 A:HIS474 4.4 23.9 1.0
ZN A:ZN907 4.5 28.1 1.0
C A:ASP171 4.6 24.5 1.0
C A:THR209 4.6 25.6 1.0
NE2 A:HIS474 4.7 24.6 1.0
C A:LYS208 4.7 23.8 1.0
S A:SO4902 4.8 77.6 1.0
CB A:ASP311 4.8 24.7 1.0
OD1 A:ASP311 5.0 26.7 1.0
CA A:GLY172 5.0 24.3 1.0
OH A:TYR306 5.0 34.8 1.0

Calcium binding site 2 out of 2 in 7g2k

Go back to Calcium Binding Sites List in 7g2k
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with 2-Chloro-5-(5- Cyclopropyloxy-2-Fluorophenyl)-4-[(4-Methyl-5-Oxo-1H-1,2,4-Triazol-3- Yl)Methoxy]Benzonitrile, I.E. Smiles C1C(Ccc(C1C1CC(C(Cl) CC1OCC1=Nnc(=O)N1C)C#N)F)OC1CC1 with IC50=0.0091413 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:22.6
occ:1.00
 O A:HOH1357 2.2 27.3 1.0
OD1 A:ASP747 2.3 22.9 1.0
O A:LEU745 2.3 21.9 1.0
OD1 A:ASN741 2.3 24.3 1.0
OD1 A:ASP739 2.3 21.3 1.0
OD1 A:ASP743 2.3 23.9 1.0
CG A:ASP743 3.3 25.0 1.0
CG A:ASN741 3.4 26.4 1.0
C A:LEU745 3.4 21.5 1.0
CG A:ASP739 3.5 21.8 1.0
CG A:ASP747 3.5 24.4 1.0
OD2 A:ASP743 3.7 27.8 1.0
ND2 A:ASN741 3.8 26.9 1.0
N A:ASP747 4.0 20.6 1.0
CA A:ASP739 4.0 19.7 1.0
C A:ARG746 4.0 22.1 1.0
N A:LEU745 4.1 21.1 1.0
O A:ARG746 4.1 22.1 1.0
CA A:ASP747 4.1 21.6 1.0
CA A:LEU745 4.2 22.1 1.0
CB A:ASP739 4.2 21.2 1.0
N A:ASP743 4.3 21.2 1.0
OD2 A:ASP747 4.4 26.0 1.0
OD2 A:ASP739 4.4 21.2 1.0
CB A:ASP747 4.4 22.2 1.0
CB A:LEU745 4.4 23.1 1.0
CB A:ASP743 4.5 24.4 1.0
N A:ARG746 4.5 22.4 1.0
N A:ASN741 4.5 22.7 1.0
O A:PHE738 4.5 19.3 1.0
C A:ASP739 4.5 20.9 1.0
OE2 A:GLU751 4.7 35.2 1.0
CB A:ASN741 4.7 23.2 1.0
CA A:ARG746 4.8 23.0 1.0
O A:HOH1351 4.8 34.0 1.0
N A:TYR742 4.8 24.7 1.0
N A:TYR740 4.8 21.9 1.0
CA A:ASP743 4.8 22.7 1.0
N A:GLY744 4.9 22.4 1.0
C A:ASN741 4.9 26.5 1.0
CA A:ASN741 4.9 25.1 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 15:33:32 2025

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