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Calcium in PDB 7g6f: Crystal Structure of Rat Autotaxin in Complex with (3R)-3-[[2-[6-(4- Acetylpiperazin-1-Yl)-4-Oxoquinazolin-3-Yl]Acetyl]Amino]-N-Methyl-3- (4-Nitrophenyl)Propanamide, I.E. Smiles C1C(Ccc(C1)[C@@H](Cc(=O)Nc) Nc(=O)CN1C=NC2CCC(CC2C1=O)N1CCN(CC1)C(=O)C)N(=O)=O with IC50=0.121117 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3R)-3-[[2-[6-(4- Acetylpiperazin-1-Yl)-4-Oxoquinazolin-3-Yl]Acetyl]Amino]-N-Methyl-3- (4-Nitrophenyl)Propanamide, I.E. Smiles C1C(Ccc(C1)[C@@H](Cc(=O)Nc) Nc(=O)CN1C=NC2CCC(CC2C1=O)N1CCN(CC1)C(=O)C)N(=O)=O with IC50=0.121117 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3R)-3-[[2-[6-(4- Acetylpiperazin-1-Yl)-4-Oxoquinazolin-3-Yl]Acetyl]Amino]-N-Methyl-3- (4-Nitrophenyl)Propanamide, I.E. Smiles C1C(Ccc(C1)[C@@H](Cc(=O)Nc) Nc(=O)CN1C=NC2CCC(CC2C1=O)N1CCN(CC1)C(=O)C)N(=O)=O with IC50=0.121117 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3R)-3-[[2-[6-(4- Acetylpiperazin-1-Yl)-4-Oxoquinazolin-3-Yl]Acetyl]Amino]-N-Methyl-3- (4-Nitrophenyl)Propanamide, I.E. Smiles C1C(Ccc(C1)[C@@H](Cc(=O)Nc) Nc(=O)CN1C=NC2CCC(CC2C1=O)N1CCN(CC1)C(=O)C)N(=O)=O with IC50=0.121117 Microm, PDB code: 7g6f 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) 48.97 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.775, 92.223, 119.988, 90, 90, 90
R / Rfree (%) 19.9 / 23.9

Other elements in 7g6f:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3R)-3-[[2-[6-(4- Acetylpiperazin-1-Yl)-4-Oxoquinazolin-3-Yl]Acetyl]Amino]-N-Methyl-3- (4-Nitrophenyl)Propanamide, I.E. Smiles C1C(Ccc(C1)[C@@H](Cc(=O)Nc) Nc(=O)CN1C=NC2CCC(CC2C1=O)N1CCN(CC1)C(=O)C)N(=O)=O with IC50=0.121117 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Potassium (K) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with (3R)-3-[[2-[6-(4- Acetylpiperazin-1-Yl)-4-Oxoquinazolin-3-Yl]Acetyl]Amino]-N-Methyl-3- (4-Nitrophenyl)Propanamide, I.E. Smiles C1C(Ccc(C1)[C@@H](Cc(=O)Nc) Nc(=O)CN1C=NC2CCC(CC2C1=O)N1CCN(CC1)C(=O)C)N(=O)=O with IC50=0.121117 Microm (pdb code 7g6f). 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 (3R)-3-[[2-[6-(4- Acetylpiperazin-1-Yl)-4-Oxoquinazolin-3-Yl]Acetyl]Amino]-N-Methyl-3- (4-Nitrophenyl)Propanamide, I.E. Smiles C1C(Ccc(C1)[C@@H](Cc(=O)Nc) Nc(=O)CN1C=NC2CCC(CC2C1=O)N1CCN(CC1)C(=O)C)N(=O)=O with IC50=0.121117 Microm, PDB code: 7g6f:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6f

Go back to Calcium Binding Sites List in 7g6f
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3R)-3-[[2-[6-(4- Acetylpiperazin-1-Yl)-4-Oxoquinazolin-3-Yl]Acetyl]Amino]-N-Methyl-3- (4-Nitrophenyl)Propanamide, I.E. Smiles C1C(Ccc(C1)[C@@H](Cc(=O)Nc) Nc(=O)CN1C=NC2CCC(CC2C1=O)N1CCN(CC1)C(=O)C)N(=O)=O with IC50=0.121117 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 (3R)-3-[[2-[6-(4- Acetylpiperazin-1-Yl)-4-Oxoquinazolin-3-Yl]Acetyl]Amino]-N-Methyl-3- (4-Nitrophenyl)Propanamide, I.E. Smiles C1C(Ccc(C1)[C@@H](Cc(=O)Nc) Nc(=O)CN1C=NC2CCC(CC2C1=O)N1CCN(CC1)C(=O)C)N(=O)=O with IC50=0.121117 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:44.4
occ:1.00
 OD1 A:ASP171 1.8 23.6 1.0
NE2 A:HIS359 2.1 20.1 1.0
OG1 A:THR209 2.1 28.4 1.0
OD2 A:ASP358 2.2 22.1 1.0
CG A:ASP171 2.8 24.5 1.0
CB A:THR209 2.9 25.4 1.0
CE1 A:HIS359 3.0 21.5 1.0
CG2 A:THR209 3.0 23.1 1.0
CD2 A:HIS359 3.1 21.5 1.0
CG A:ASP358 3.1 22.1 1.0
OD2 A:ASP171 3.2 34.2 1.0
CA A:THR209 3.4 24.8 1.0
O A:HOH1070 3.4 31.6 1.0
OD1 A:ASP358 3.4 20.7 1.0
N A:THR209 4.0 23.0 1.0
CB A:ASP171 4.1 23.0 1.0
ND1 A:HIS359 4.1 20.6 1.0
CG A:HIS359 4.2 20.8 1.0
OD1 A:ASP311 4.2 24.8 1.0
N A:GLY172 4.3 20.0 1.0
CE1 A:HIS474 4.3 17.9 1.0
CA A:ASP171 4.3 19.7 1.0
CG A:ASP311 4.3 28.9 1.0
CB A:ASP358 4.4 19.8 1.0
O A:HOH1384 4.5 27.7 1.0
ZN A:ZN905 4.5 24.0 1.0
O A:HOH1001 4.5 37.6 1.0
NE2 A:HIS474 4.5 16.1 1.0
C A:ASP171 4.6 20.5 1.0
OD2 A:ASP311 4.7 31.3 1.0
C A:THR209 4.7 23.4 1.0
CB A:ASP311 4.8 23.6 1.0
C A:LYS208 4.8 23.2 1.0
O A:HOH1226 5.0 29.6 1.0

Calcium binding site 2 out of 2 in 7g6f

Go back to Calcium Binding Sites List in 7g6f
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3R)-3-[[2-[6-(4- Acetylpiperazin-1-Yl)-4-Oxoquinazolin-3-Yl]Acetyl]Amino]-N-Methyl-3- (4-Nitrophenyl)Propanamide, I.E. Smiles C1C(Ccc(C1)[C@@H](Cc(=O)Nc) Nc(=O)CN1C=NC2CCC(CC2C1=O)N1CCN(CC1)C(=O)C)N(=O)=O with IC50=0.121117 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 (3R)-3-[[2-[6-(4- Acetylpiperazin-1-Yl)-4-Oxoquinazolin-3-Yl]Acetyl]Amino]-N-Methyl-3- (4-Nitrophenyl)Propanamide, I.E. Smiles C1C(Ccc(C1)[C@@H](Cc(=O)Nc) Nc(=O)CN1C=NC2CCC(CC2C1=O)N1CCN(CC1)C(=O)C)N(=O)=O with IC50=0.121117 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:19.5
occ:1.00
 OD1 A:ASP747 2.2 19.5 1.0
OD1 A:ASP739 2.3 20.5 1.0
OD1 A:ASP743 2.3 20.2 1.0
O A:HOH1377 2.3 20.5 1.0
O A:LEU745 2.4 16.1 1.0
OD1 A:ASN741 2.4 21.9 1.0
CG A:ASP743 3.3 21.8 1.0
CG A:ASN741 3.5 24.8 1.0
CG A:ASP739 3.5 19.7 1.0
CG A:ASP747 3.5 21.3 1.0
C A:LEU745 3.5 18.1 1.0
OD2 A:ASP743 3.6 24.5 1.0
ND2 A:ASN741 3.9 24.6 1.0
N A:ASP747 3.9 21.1 1.0
CA A:ASP739 4.0 18.6 1.0
N A:LEU745 4.0 16.8 1.0
C A:ARG746 4.1 22.2 1.0
CA A:ASP747 4.2 22.2 1.0
O A:ARG746 4.2 21.1 1.0
CA A:LEU745 4.2 16.5 1.0
CB A:ASP739 4.3 18.5 1.0
N A:ASP743 4.3 20.7 1.0
O A:HOH1156 4.3 30.1 1.0
OD2 A:ASP747 4.3 23.7 1.0
OD2 A:ASP739 4.3 18.9 1.0
CB A:LEU745 4.4 17.3 1.0
CB A:ASP747 4.4 21.9 1.0
CB A:ASP743 4.5 20.5 1.0
N A:ARG746 4.5 17.5 1.0
O A:PHE738 4.5 20.0 1.0
C A:ASP739 4.5 19.9 1.0
N A:ASN741 4.6 21.6 1.0
CA A:ARG746 4.7 20.3 1.0
CA A:ASP743 4.8 20.1 1.0
N A:GLY744 4.8 19.1 1.0
CB A:ASN741 4.8 22.4 1.0
N A:TYR742 4.8 20.9 1.0
N A:TYR740 4.9 19.0 1.0
OE2 A:GLU751 4.9 34.4 1.0
C A:ASN741 4.9 20.1 1.0
C A:ASP743 5.0 19.8 1.0
CA A:ASN741 5.0 22.3 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 15:55:30 2025

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