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Calcium in PDB 7g5n: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm, PDB code: 7g5n was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.70 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.932, 91.4, 118.69, 90, 90, 90
R / Rfree (%) 18.4 / 21.5

Other elements in 7g5n:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm (pdb code 7g5n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm, PDB code: 7g5n:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7g5n

Go back to Calcium Binding Sites List in 7g5n
Calcium binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:16.1
occ:1.00
 O A:LEU745 2.3 13.7 1.0
OD1 A:ASP747 2.3 17.6 1.0
OD1 A:ASN741 2.3 16.2 1.0
OD1 A:ASP743 2.3 15.8 1.0
O A:HOH1417 2.3 20.3 1.0
OD1 A:ASP739 2.3 15.2 1.0
CG A:ASP743 3.3 17.2 1.0
CG A:ASN741 3.4 20.2 1.0
CG A:ASP739 3.5 16.0 1.0
C A:LEU745 3.5 13.9 1.0
CG A:ASP747 3.5 16.6 1.0
OD2 A:ASP743 3.8 21.1 1.0
N A:ASP747 3.9 15.2 1.0
ND2 A:ASN741 3.9 21.9 1.0
CA A:ASP739 3.9 13.7 1.0
C A:ARG746 4.0 17.4 1.0
N A:LEU745 4.1 13.9 1.0
CA A:ASP747 4.1 16.0 1.0
CB A:ASP739 4.2 15.2 1.0
O A:ARG746 4.2 16.0 1.0
CA A:LEU745 4.2 13.7 1.0
N A:ASP743 4.3 16.5 1.0
OD2 A:ASP739 4.4 15.4 1.0
OD2 A:ASP747 4.4 19.6 1.0
O A:PHE738 4.4 13.9 1.0
CB A:ASP747 4.4 15.3 1.0
N A:ASN741 4.4 15.5 1.0
CB A:LEU745 4.5 14.8 1.0
C A:ASP739 4.5 13.9 1.0
N A:ARG746 4.5 14.6 1.0
CB A:ASP743 4.5 16.7 1.0
OE2 A:GLU751 4.6 30.5 1.0
CB A:ASN741 4.7 17.2 1.0
CA A:ARG746 4.7 16.0 1.0
N A:TYR740 4.7 13.5 1.0
N A:TYR742 4.7 17.7 1.0
O A:HOH1397 4.8 33.7 1.0
CA A:ASP743 4.8 16.6 1.0
N A:GLY744 4.8 16.5 1.0
C A:ASN741 4.8 16.0 1.0
CA A:ASN741 4.8 16.8 1.0

Calcium binding site 2 out of 3 in 7g5n

Go back to Calcium Binding Sites List in 7g5n
Calcium binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:23.1
occ:1.00
 O A:ASP672 2.2 22.5 1.0
O A:MET675 2.3 21.7 1.0
O A:TYR669 2.3 24.3 1.0
O A:HOH1298 2.4 25.6 1.0
O A:HOH1436 2.4 32.8 1.0
O A:HOH1433 2.6 36.8 1.0
C A:ASP672 3.4 24.5 1.0
C A:TYR669 3.4 23.5 1.0
C A:MET675 3.4 21.4 1.0
N A:MET675 4.1 23.5 1.0
CA A:TYR669 4.2 20.9 1.0
O A:LYS670 4.2 30.5 1.0
CA A:LYS673 4.3 28.3 1.0
CA A:MET675 4.3 21.1 1.0
N A:SER676 4.3 18.8 1.0
N A:LYS673 4.3 26.3 1.0
CA A:ASP672 4.4 24.6 1.0
CA A:SER676 4.4 20.2 1.0
C A:LYS673 4.4 26.9 1.0
N A:LYS670 4.4 22.3 1.0
O A:HOH1089 4.5 33.5 1.0
N A:ASP672 4.5 26.1 1.0
C A:LYS670 4.5 26.7 1.0
CB A:ASP672 4.6 25.3 1.0
CA A:LYS670 4.6 27.6 1.0
O A:LYS673 4.6 29.6 1.0
CB A:TYR669 4.6 19.8 1.0
N A:GLN674 4.8 25.1 1.0
C A:GLN674 4.9 25.0 1.0
CB A:SER676 4.9 20.5 1.0

Calcium binding site 3 out of 3 in 7g5n

Go back to Calcium Binding Sites List in 7g5n
Calcium binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-(4-Methoxynaphthalene-2-Carbonyl)-4,9- Diazatricyclo[5.3.0.02,6]Decan-4-Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1)C(=O)C1CCC2C(C1)N=NN2)C(=O) C1CC(C2C(C1)CCCC2)Oc with IC50=0.0878229 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:44.4
occ:1.00
 OG1 A:THR209 2.5 25.5 1.0
NE2 A:HIS359 2.6 15.7 1.0
OD1 A:ASP171 2.6 24.5 1.0
ZN A:ZN904 2.7 18.7 1.0
N25 A:Y3F901 3.0 22.4 1.0
OD1 A:ASP311 3.0 19.4 1.0
CE1 A:HIS359 3.1 16.7 1.0
OD2 A:ASP171 3.2 28.4 1.0
NE2 A:HIS474 3.2 16.0 1.0
CE1 A:HIS474 3.2 17.5 1.0
CG A:ASP171 3.3 23.1 1.0
C24 A:Y3F901 3.3 23.9 1.0
C21 A:Y3F901 3.4 25.9 1.0
CB A:THR209 3.4 20.9 1.0
CG2 A:THR209 3.4 20.3 1.0
CG A:ASP311 3.4 18.4 1.0
OD2 A:ASP311 3.7 21.9 1.0
CD2 A:HIS359 3.9 16.1 1.0
CA A:THR209 4.0 17.5 1.0
N26 A:Y3F901 4.0 27.9 1.0
OD2 A:ASP358 4.1 23.4 1.0
N A:THR209 4.2 16.5 1.0
ND1 A:HIS474 4.3 16.6 1.0
CD2 A:HIS474 4.3 15.2 1.0
CB A:ASP311 4.4 16.1 1.0
ND1 A:HIS359 4.4 16.0 1.0
C23 A:Y3F901 4.5 26.0 1.0
C20 A:Y3F901 4.5 27.8 1.0
N27 A:Y3F901 4.8 29.0 1.0
CB A:ASP171 4.8 18.1 1.0
CG A:HIS359 4.8 16.8 1.0
NE2 A:HIS315 4.8 19.8 1.0
CG A:HIS474 4.8 14.6 1.0
CG A:ASP358 4.9 19.9 1.0
N A:GLY172 4.9 15.7 1.0
OD1 A:ASP358 5.0 16.5 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 15:51:43 2025

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