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Calcium 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
Sodium (Na) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 7g6w

Go back to Calcium Binding Sites List in 7g6w
Calcium 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 Calcium with other atoms in the Ca 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:Ca904

b:29.6
occ:1.00
 OD1 A:ASP171 1.8 26.2 1.0
OG1 A:THR209 2.0 27.5 1.0
NE2 A:HIS359 2.1 19.0 1.0
OD2 A:ASP358 2.2 22.0 1.0
CG A:ASP171 2.8 27.6 1.0
CB A:THR209 2.9 24.4 1.0
CE1 A:HIS359 3.0 18.0 1.0
CG A:ASP358 3.1 22.2 1.0
CD2 A:HIS359 3.1 18.4 1.0
OD2 A:ASP171 3.1 36.7 1.0
CG2 A:THR209 3.2 24.5 1.0
CA A:THR209 3.3 21.1 1.0
OD1 A:ASP358 3.3 20.3 1.0
O A:HOH1066 3.8 35.1 1.0
N A:THR209 3.8 18.9 1.0
OD2 A:ASP311 4.1 23.8 1.0
CB A:ASP171 4.1 22.7 1.0
ND1 A:HIS359 4.1 17.6 1.0
N A:GLY172 4.1 20.1 1.0
CG A:HIS359 4.2 16.8 1.0
O A:HOH1013 4.2 34.1 1.0
CA A:ASP171 4.3 21.1 1.0
CB A:ASP358 4.4 18.8 1.0
CE1 A:HIS474 4.4 18.3 1.0
CG A:ASP311 4.5 21.2 1.0
ZN A:ZN906 4.5 23.1 1.0
O A:HOH1482 4.5 28.3 1.0
NE2 A:HIS474 4.6 20.5 1.0
C A:THR209 4.6 19.5 1.0
C A:ASP171 4.6 21.5 1.0
C A:LYS208 4.7 19.9 1.0
CB A:ASP311 4.9 20.2 1.0
OD1 A:ASP311 5.0 23.7 1.0
CA A:GLY172 5.0 20.9 1.0

Calcium binding site 2 out of 2 in 7g6w

Go back to Calcium Binding Sites List in 7g6w
Calcium 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 Calcium with other atoms in the Ca 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:Ca908

b:20.3
occ:1.00
 OD1 A:ASP747 2.3 19.5 1.0
O A:HOH1445 2.3 23.9 1.0
OD1 A:ASP739 2.3 18.4 1.0
OD1 A:ASN741 2.3 24.6 1.0
O A:LEU745 2.3 19.4 1.0
OD1 A:ASP743 2.4 22.3 1.0
CG A:ASP743 3.4 21.8 1.0
CG A:ASN741 3.4 23.4 1.0
C A:LEU745 3.5 17.8 1.0
CG A:ASP739 3.5 18.6 1.0
CG A:ASP747 3.5 20.9 1.0
OD2 A:ASP743 3.8 25.3 1.0
ND2 A:ASN741 3.9 23.8 1.0
N A:ASP747 3.9 18.7 1.0
CA A:ASP739 3.9 16.7 1.0
C A:ARG746 4.1 18.0 1.0
N A:LEU745 4.1 17.3 1.0
CA A:ASP747 4.2 19.7 1.0
CA A:LEU745 4.2 17.8 1.0
CB A:ASP739 4.2 16.6 1.0
O A:ARG746 4.2 17.6 1.0
N A:ASP743 4.3 18.8 1.0
OD2 A:ASP747 4.4 22.7 1.0
N A:ASN741 4.4 19.8 1.0
CB A:ASP747 4.4 17.9 1.0
OD2 A:ASP739 4.4 17.7 1.0
C A:ASP739 4.4 19.1 1.0
CB A:LEU745 4.4 19.6 1.0
O A:PHE738 4.4 16.7 1.0
N A:ARG746 4.5 17.0 1.0
CB A:ASP743 4.6 20.4 1.0
OE2 A:GLU751 4.6 31.6 1.0
N A:TYR742 4.7 19.2 1.0
N A:TYR740 4.7 19.0 1.0
CB A:ASN741 4.7 20.6 1.0
CA A:ARG746 4.7 17.8 1.0
O A:HOH1404 4.7 34.9 1.0
C A:ASN741 4.8 20.2 1.0
N A:GLY744 4.8 22.1 1.0
CA A:ASP743 4.8 21.2 1.0
CA A:ASN741 4.9 20.6 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: Wed Jul 9 22:35:30 2025

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