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Calcium in PDB 7g6d: Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm, PDB code: 7g6d 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) 45.84 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.142, 91.682, 119.036, 90, 90, 90
R / Rfree (%) 19.2 / 23

Other elements in 7g6d:

The structure of Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm (pdb code 7g6d). 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 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm, PDB code: 7g6d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6d

Go back to Calcium Binding Sites List in 7g6d
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 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 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:39.4
occ:1.00
 OG1 A:THR209 1.8 27.0 1.0
OD1 A:ASP171 2.0 28.3 1.0
NE2 A:HIS359 2.1 17.6 1.0
OD2 A:ASP358 2.4 25.7 1.0
CG A:ASP171 2.7 26.4 1.0
OD2 A:ASP171 2.9 33.8 1.0
CB A:THR209 2.9 22.7 1.0
CE1 A:HIS359 3.0 18.1 1.0
CD2 A:HIS359 3.0 18.9 1.0
CG A:ASP358 3.2 24.8 1.0
OD1 A:ASP358 3.3 21.2 1.0
CG2 A:THR209 3.4 23.6 1.0
CA A:THR209 3.4 21.9 1.0
N A:THR209 3.8 20.2 1.0
CB A:ASP171 4.0 22.4 1.0
ND1 A:HIS359 4.1 18.1 1.0
CG A:HIS359 4.1 18.1 1.0
OD1 A:ASP311 4.2 25.1 1.0
N A:GLY172 4.2 19.6 1.0
O A:HOH1006 4.3 26.8 1.0
CA A:ASP171 4.3 22.3 1.0
CE1 A:HIS474 4.4 19.1 1.0
CG A:ASP311 4.5 21.3 1.0
CB A:ASP358 4.5 21.3 1.0
ZN A:ZN906 4.5 22.8 1.0
NE2 A:HIS474 4.6 19.9 1.0
C A:LYS208 4.6 21.3 1.0
C A:ASP171 4.6 21.9 1.0
C A:THR209 4.7 20.6 1.0
O A:HOH1440 4.8 33.8 1.0
OD2 A:ASP311 4.8 23.9 1.0
CB A:ASP311 4.9 22.2 1.0
OH A:TYR306 4.9 29.0 1.0

Calcium binding site 2 out of 2 in 7g6d

Go back to Calcium Binding Sites List in 7g6d
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 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 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:20.1
occ:1.00
 OD1 A:ASP747 2.3 20.1 1.0
O A:HOH1435 2.3 25.3 1.0
O A:LEU745 2.3 19.4 1.0
OD1 A:ASN741 2.3 22.6 1.0
OD1 A:ASP739 2.4 19.3 1.0
OD1 A:ASP743 2.4 21.3 1.0
CG A:ASP743 3.3 21.7 1.0
CG A:ASN741 3.5 25.7 1.0
C A:LEU745 3.5 19.9 1.0
CG A:ASP747 3.5 20.7 1.0
CG A:ASP739 3.5 18.6 1.0
OD2 A:ASP743 3.8 23.4 1.0
CA A:ASP739 3.9 17.1 1.0
N A:ASP747 3.9 17.2 1.0
ND2 A:ASN741 3.9 24.7 1.0
C A:ARG746 4.0 18.8 1.0
N A:LEU745 4.1 17.9 1.0
CA A:ASP747 4.1 19.9 1.0
O A:ARG746 4.1 18.6 1.0
CB A:ASP739 4.2 18.6 1.0
CA A:LEU745 4.2 18.6 1.0
N A:ASP743 4.3 18.2 1.0
OD2 A:ASP747 4.4 21.2 1.0
O A:PHE738 4.4 17.4 1.0
CB A:ASP747 4.4 18.5 1.0
OD2 A:ASP739 4.4 19.4 1.0
C A:ASP739 4.4 18.2 1.0
N A:ASN741 4.5 20.2 1.0
N A:ARG746 4.5 19.4 1.0
CB A:LEU745 4.5 19.7 1.0
CB A:ASP743 4.6 19.9 1.0
OE2 A:GLU751 4.6 33.6 1.0
N A:TYR740 4.7 18.3 1.0
CA A:ARG746 4.7 17.8 1.0
N A:TYR742 4.7 18.9 1.0
CB A:ASN741 4.8 21.7 1.0
CA A:ASP743 4.8 18.2 1.0
O A:HOH1419 4.8 37.6 1.0
C A:ASN741 4.9 20.6 1.0
N A:GLY744 4.9 19.8 1.0
CA A:ASN741 4.9 20.0 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 15:55:17 2025

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