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Calcium in PDB 7g4y: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 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,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm, PDB code: 7g4y 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) 45.82 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.948, 91.632, 119.854, 90, 90, 90
R / Rfree (%) 18.4 / 22.5

Other elements in 7g4y:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Sodium (Na) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm (pdb code 7g4y). 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm, PDB code: 7g4y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g4y

Go back to Calcium Binding Sites List in 7g4y
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 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,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:20.6
occ:1.00
 O A:HOH1392 2.2 23.5 1.0
O A:LEU745 2.3 19.4 1.0
OD1 A:ASP747 2.3 19.6 1.0
OD1 A:ASP739 2.3 19.1 1.0
OD1 A:ASN741 2.3 23.1 1.0
OD1 A:ASP743 2.4 24.5 1.0
CG A:ASP743 3.3 23.7 1.0
CG A:ASN741 3.4 24.4 1.0
C A:LEU745 3.4 21.0 1.0
CG A:ASP739 3.5 20.5 1.0
CG A:ASP747 3.5 20.1 1.0
OD2 A:ASP743 3.7 25.0 1.0
ND2 A:ASN741 3.9 26.1 1.0
N A:ASP747 3.9 21.2 1.0
CA A:ASP739 4.0 20.2 1.0
C A:ARG746 4.0 21.2 1.0
N A:LEU745 4.1 18.6 1.0
CA A:ASP747 4.1 20.2 1.0
O A:ARG746 4.2 22.1 1.0
CA A:LEU745 4.2 20.9 1.0
CB A:ASP739 4.2 21.2 1.0
N A:ASP743 4.3 21.4 1.0
OD2 A:ASP747 4.4 22.1 1.0
O A:PHE738 4.4 18.9 1.0
CB A:ASP747 4.4 19.6 1.0
OD2 A:ASP739 4.4 21.2 1.0
N A:ARG746 4.5 19.4 1.0
N A:ASN741 4.5 21.2 1.0
C A:ASP739 4.5 21.4 1.0
CB A:LEU745 4.5 21.7 1.0
CB A:ASP743 4.5 21.4 1.0
CA A:ARG746 4.6 21.1 0.5
OE2 A:GLU751 4.7 34.8 1.0
N A:TYR740 4.7 21.6 1.0
CA A:ARG746 4.7 20.3 0.5
CB A:ASN741 4.7 21.2 1.0
N A:TYR742 4.8 21.8 1.0
CA A:ASP743 4.8 21.7 1.0
O A:HOH1391 4.9 39.7 1.0
C A:ASN741 4.9 22.2 1.0
N A:GLY744 4.9 20.9 1.0
CA A:ASN741 4.9 21.1 1.0

Calcium binding site 2 out of 2 in 7g4y

Go back to Calcium Binding Sites List in 7g4y
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 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,2S,6R,7S)-9-[4-Propan-2-Yloxy-7-(Trifluoromethyl) Quinoline-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)C1NC2C(C(C1)Oc(C)C)Ccc(C2)C(F)(F)F with IC50=0.0197138 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:45.4
occ:1.00
 OD1 A:ASP171 1.9 27.5 1.0
OG1 A:THR209 2.0 29.5 1.0
NE2 A:HIS359 2.2 20.5 1.0
OD2 A:ASP358 2.2 24.1 1.0
CG A:ASP171 2.8 27.4 1.0
CB A:THR209 2.8 25.6 1.0
CG2 A:THR209 3.0 26.7 1.0
CG A:ASP358 3.1 21.5 1.0
CE1 A:HIS359 3.1 20.0 1.0
OD2 A:ASP171 3.1 37.8 1.0
CD2 A:HIS359 3.2 20.7 1.0
CA A:THR209 3.3 22.2 1.0
OD1 A:ASP358 3.3 20.2 1.0
N A:THR209 3.9 21.3 1.0
CB A:ASP171 4.1 23.2 1.0
C21 A:YDE901 4.1 33.7 1.0
O A:HOH1010 4.2 35.5 1.0
OD1 A:ASP311 4.2 23.7 1.0
ND1 A:HIS359 4.2 18.9 1.0
CG A:HIS359 4.2 20.3 1.0
N A:GLY172 4.3 20.3 1.0
CE1 A:HIS474 4.3 20.5 1.0
CB A:ASP358 4.4 20.0 1.0
CA A:ASP171 4.4 21.6 1.0
N25 A:YDE901 4.4 30.5 1.0
C24 A:YDE901 4.4 35.3 1.0
ZN A:ZN902 4.5 23.2 1.0
CG A:ASP311 4.5 23.8 1.0
C A:THR209 4.6 22.9 1.0
NE2 A:HIS474 4.6 22.2 1.0
C A:LYS208 4.7 21.5 1.0
C A:ASP171 4.7 21.7 1.0
O A:THR209 4.9 22.4 1.0
C20 A:YDE901 4.9 38.9 1.0
CB A:ASP311 5.0 22.0 1.0
OD2 A:ASP311 5.0 25.6 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: Sat Feb 8 15:48:03 2025

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