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Sodium in PDB 7g6w: Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(Oxolan-3-Ylmethyl)Piperazin-1- Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles O=C1N(Cc(=O)NCC2CC(Cl) C(Cl)CC2)C=NC2C1CC(N1CCN(C[C@H]3CCOC3)CC1)CC2 with IC50=0.0358891 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(Oxolan-3-Ylmethyl)Piperazin-1- Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles O=C1N(Cc(=O)NCC2CC(Cl) C(Cl)CC2)C=NC2C1CC(N1CCN(C[C@H]3CCOC3)CC1)CC2 with IC50=0.0358891 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(Oxolan-3-Ylmethyl)Piperazin-1- Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles O=C1N(Cc(=O)NCC2CC(Cl) C(Cl)CC2)C=NC2C1CC(N1CCN(C[C@H]3CCOC3)CC1)CC2 with IC50=0.0358891 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(Oxolan-3-Ylmethyl)Piperazin-1- Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles O=C1N(Cc(=O)NCC2CC(Cl) C(Cl)CC2)C=NC2C1CC(N1CCN(C[C@H]3CCOC3)CC1)CC2 with IC50=0.0358891 Microm, PDB code: 7g6w was solved by M.Stihle, J.Benz, D.Hunziker, E.Martin-Rainer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.91 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.963, 91.824, 119.643, 90, 90, 90
R / Rfree (%) 18.4 / 22.3

Other elements in 7g6w:

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(Oxolan-3-Ylmethyl)Piperazin-1- Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles O=C1N(Cc(=O)NCC2CC(Cl) C(Cl)CC2)C=NC2C1CC(N1CCN(C[C@H]3CCOC3)CC1)CC2 with IC50=0.0358891 Microm also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 1 atom
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(Oxolan-3-Ylmethyl)Piperazin-1- Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles O=C1N(Cc(=O)NCC2CC(Cl) C(Cl)CC2)C=NC2C1CC(N1CCN(C[C@H]3CCOC3)CC1)CC2 with IC50=0.0358891 Microm (pdb code 7g6w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(Oxolan-3-Ylmethyl)Piperazin-1- Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles O=C1N(Cc(=O)NCC2CC(Cl) C(Cl)CC2)C=NC2C1CC(N1CCN(C[C@H]3CCOC3)CC1)CC2 with IC50=0.0358891 Microm, PDB code: 7g6w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g6w

Go back to Sodium Binding Sites List in 7g6w
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(Oxolan-3-Ylmethyl)Piperazin-1- Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles O=C1N(Cc(=O)NCC2CC(Cl) C(Cl)CC2)C=NC2C1CC(N1CCN(C[C@H]3CCOC3)CC1)CC2 with IC50=0.0358891 Microm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(Oxolan-3-Ylmethyl)Piperazin-1- Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles O=C1N(Cc(=O)NCC2CC(Cl) C(Cl)CC2)C=NC2C1CC(N1CCN(C[C@H]3CCOC3)CC1)CC2 with IC50=0.0358891 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:29.7
occ:1.00
 OG A:SER807 2.3 23.1 1.0
O A:HOH1479 2.3 29.1 1.0
O A:HOH1314 2.4 30.5 1.0
O A:SER804 2.4 23.9 1.0
O A:ASN801 2.5 20.8 1.0
O A:HOH1317 2.5 32.1 1.0
C A:ASN801 3.4 22.6 1.0
CB A:SER807 3.5 24.1 1.0
C A:SER804 3.5 23.9 1.0
CA A:ASP802 3.8 25.3 1.0
N A:ASP802 4.0 24.0 1.0
N A:SER807 4.1 26.9 1.0
C A:ASP802 4.1 25.1 1.0
O A:ASP802 4.1 24.1 1.0
CA A:CYS805 4.2 27.3 1.0
N A:CYS805 4.3 24.4 1.0
CA A:SER807 4.3 27.1 1.0
O A:HOH1172 4.3 33.6 1.0
N A:SER804 4.4 21.3 1.0
C A:CYS805 4.4 26.1 1.0
CB A:ASN801 4.4 20.8 1.0
O A:CYS805 4.4 29.1 1.0
CA A:SER804 4.5 20.6 1.0
CA A:ASN801 4.5 21.3 1.0
O A:HOH1517 4.6 49.5 1.0
O A:HOH1276 4.7 36.2 1.0
OD1 A:ASP802 4.7 32.8 1.0
O A:HOH1269 4.7 33.6 1.0
CB A:SER804 4.8 22.4 1.0
N A:GLU803 4.9 22.5 1.0
N A:ASN806 5.0 26.1 1.0

Sodium binding site 2 out of 2 in 7g6w

Go back to Sodium Binding Sites List in 7g6w
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(Oxolan-3-Ylmethyl)Piperazin-1- Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles O=C1N(Cc(=O)NCC2CC(Cl) C(Cl)CC2)C=NC2C1CC(N1CCN(C[C@H]3CCOC3)CC1)CC2 with IC50=0.0358891 Microm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with N-[(3,4- Dichlorophenyl)Methyl]-2-[4-Oxo-6-[4-(Oxolan-3-Ylmethyl)Piperazin-1- Yl]Quinazolin-3-Yl]Acetamide, I.E. Smiles O=C1N(Cc(=O)NCC2CC(Cl) C(Cl)CC2)C=NC2C1CC(N1CCN(C[C@H]3CCOC3)CC1)CC2 with IC50=0.0358891 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:34.2
occ:1.00
 O A:TYR669 2.3 28.8 1.0
O A:MET675 2.3 27.6 1.0
O A:ASP672 2.3 31.0 1.0
O A:HOH1436 2.4 35.2 1.0
O A:HOH1529 2.9 46.4 1.0
C A:TYR669 3.4 30.4 1.0
C A:MET675 3.5 26.8 1.0
C A:ASP672 3.5 33.6 1.0
N A:MET675 4.1 29.1 1.0
CA A:TYR669 4.2 26.7 1.0
O A:HOH1547 4.3 46.5 1.0
O A:LYS670 4.3 37.0 1.0
CA A:MET675 4.3 25.8 1.0
CA A:LYS673 4.4 36.1 1.0
N A:SER676 4.4 22.1 1.0
N A:LYS673 4.4 31.5 1.0
CA A:SER676 4.4 21.9 1.0
N A:LYS670 4.4 32.0 1.0
CA A:ASP672 4.4 31.4 1.0
C A:LYS673 4.5 34.1 1.0
CB A:TYR669 4.5 25.3 1.0
N A:ASP672 4.5 35.1 1.0
C A:LYS670 4.6 33.9 1.0
O A:LYS673 4.6 33.4 1.0
CA A:LYS670 4.6 34.9 1.0
CB A:ASP672 4.6 30.9 1.0
N A:GLN674 4.9 32.1 1.0
CB A:MET675 5.0 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 23:30:33 2025

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