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Calcium in PDB 7g5p: Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm, PDB code: 7g5p was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.03 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.203, 92.065, 119.91, 90, 90, 90
R / Rfree (%) 18.5 / 21.5

Other elements in 7g5p:

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Sodium (Na) 2 atoms
Fluorine (F) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm (pdb code 7g5p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm, PDB code: 7g5p:

Calcium binding site 1 out of 1 in 7g5p

Go back to Calcium Binding Sites List in 7g5p
Calcium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 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 N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:13.5
occ:1.00
 O A:HOH1485 2.2 16.3 1.0
OD1 A:ASP747 2.3 16.4 1.0
OD1 A:ASN741 2.3 16.5 1.0
OD1 A:ASP739 2.3 11.6 1.0
O A:LEU745 2.3 13.6 1.0
OD1 A:ASP743 2.4 14.0 1.0
CG A:ASP743 3.3 15.6 1.0
CG A:ASN741 3.4 17.2 1.0
C A:LEU745 3.5 13.0 1.0
CG A:ASP739 3.5 11.9 1.0
CG A:ASP747 3.5 14.6 1.0
OD2 A:ASP743 3.7 17.6 1.0
ND2 A:ASN741 3.9 19.5 1.0
CA A:ASP739 4.0 11.9 1.0
N A:ASP747 4.0 12.0 1.0
C A:ARG746 4.1 13.8 1.0
N A:LEU745 4.1 12.0 1.0
CA A:ASP747 4.1 13.3 1.0
CB A:ASP739 4.2 12.0 1.0
CA A:LEU745 4.2 13.1 1.0
O A:ARG746 4.2 14.3 1.0
N A:ASP743 4.3 12.7 1.0
OD2 A:ASP739 4.4 11.4 1.0
OD2 A:ASP747 4.4 16.0 1.0
CB A:LEU745 4.4 14.8 1.0
CB A:ASP747 4.4 14.0 1.0
O A:PHE738 4.5 12.5 1.0
N A:ASN741 4.5 12.3 1.0
C A:ASP739 4.5 12.6 1.0
N A:ARG746 4.5 13.1 1.0
CB A:ASP743 4.5 13.7 1.0
OE2 A:GLU751 4.6 23.9 1.0
CB A:ASN741 4.7 14.4 1.0
N A:TYR740 4.7 12.9 1.0
O A:HOH1473 4.7 26.0 1.0
CA A:ARG746 4.7 12.8 1.0
N A:TYR742 4.8 14.2 1.0
CA A:ASP743 4.8 13.2 1.0
C A:ASN741 4.8 14.2 1.0
N A:GLY744 4.9 12.5 1.0
CA A:ASN741 4.9 13.0 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 15:51:35 2025

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