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Calcium in PDB 7g6k: Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm, PDB code: 7g6k 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) 49.27 / 2.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.689, 92.202, 121.149, 90, 90, 90
R / Rfree (%) 19.5 / 24.4

Other elements in 7g6k:

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 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 [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm (pdb code 7g6k). 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 [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm, PDB code: 7g6k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6k

Go back to Calcium Binding Sites List in 7g6k
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 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 [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:70.5
occ:1.00
 OG1 A:THR209 1.9 42.1 1.0
OD1 A:ASP171 2.1 38.5 1.0
NE2 A:HIS359 2.1 27.7 1.0
CE1 A:HIS359 2.8 26.9 1.0
CG A:ASP171 3.0 36.1 1.0
OD2 A:ASP358 3.1 38.6 1.0
OD2 A:ASP171 3.2 39.8 1.0
CB A:THR209 3.2 37.0 1.0
CD2 A:HIS359 3.3 27.1 1.0
OD2 A:ASP311 3.4 33.2 1.0
N34 A:Y9L901 3.7 47.2 1.0
ZN A:ZN905 3.7 31.6 1.0
CG2 A:THR209 3.7 37.6 1.0
CA A:THR209 3.7 35.3 1.0
CE1 A:HIS474 3.7 28.5 1.0
C30 A:Y9L901 3.8 51.3 1.0
C33 A:Y9L901 3.8 49.8 1.0
NE2 A:HIS474 3.8 28.2 1.0
CG A:ASP358 3.8 34.6 1.0
CG A:ASP311 3.9 33.4 1.0
OD1 A:ASP358 3.9 34.7 1.0
ND1 A:HIS359 4.0 27.1 1.0
N A:THR209 4.1 34.0 1.0
CG A:HIS359 4.3 27.4 1.0
CB A:ASP171 4.3 33.8 1.0
OD1 A:ASP311 4.4 35.1 1.0
N A:GLY172 4.4 29.4 1.0
CB A:ASP311 4.5 32.3 1.0
ND1 A:HIS474 4.6 29.8 1.0
C35 A:Y9L901 4.7 48.3 1.0
CD2 A:HIS474 4.7 28.6 1.0
C29 A:Y9L901 4.8 53.6 1.0
CA A:ASP171 4.8 31.4 1.0
C32 A:Y9L901 4.8 51.4 1.0
C A:LYS208 4.9 33.2 1.0
C A:ASP171 4.9 30.8 1.0

Calcium binding site 2 out of 2 in 7g6k

Go back to Calcium Binding Sites List in 7g6k
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 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 [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(2-Oxo-1H-[1,3]Oxazolo[5, 4-B]Pyridine-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@@H]1CN(C2)C(=O) OCC1CCC(CC1)Oc(F)(F)F)C(=O)C1CCC2C(N1)Oc(=O)N2 with IC50=0.00908453 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:28.9
occ:1.00
 O A:HOH1282 2.2 34.5 1.0
OD1 A:ASP747 2.3 30.6 1.0
OD1 A:ASP739 2.3 25.8 1.0
OD1 A:ASN741 2.3 34.9 1.0
OD1 A:ASP743 2.3 32.3 1.0
O A:LEU745 2.3 30.1 1.0
CG A:ASP743 3.3 32.8 1.0
CG A:ASN741 3.4 34.4 1.0
C A:LEU745 3.5 32.1 1.0
CG A:ASP739 3.5 26.2 1.0
CG A:ASP747 3.5 32.5 1.0
OD2 A:ASP743 3.6 33.0 1.0
ND2 A:ASN741 3.8 33.3 1.0
N A:ASP747 4.0 31.7 1.0
CA A:ASP739 4.0 28.6 1.0
N A:LEU745 4.0 30.9 1.0
C A:ARG746 4.1 33.4 1.0
CA A:LEU745 4.2 31.9 1.0
CB A:ASP739 4.2 26.4 1.0
CA A:ASP747 4.2 32.2 1.0
O A:ARG746 4.3 34.3 1.0
OD2 A:ASP747 4.3 34.2 1.0
N A:ASP743 4.3 31.2 1.0
OD2 A:ASP739 4.4 25.4 1.0
CB A:LEU745 4.5 33.0 1.0
CB A:ASP747 4.5 31.4 1.0
O A:PHE738 4.5 27.4 1.0
N A:ARG746 4.5 31.2 1.0
C A:ASP739 4.5 29.8 1.0
N A:ASN741 4.5 31.7 1.0
CB A:ASP743 4.6 30.1 1.0
CB A:ASN741 4.7 32.3 1.0
N A:TYR742 4.7 33.1 1.0
CA A:ARG746 4.7 32.8 1.0
N A:GLY744 4.8 29.8 1.0
N A:TYR740 4.8 29.1 1.0
CA A:ASP743 4.9 30.7 1.0
CA A:ASN741 4.9 32.6 1.0
C A:ASN741 4.9 33.6 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 15:55:30 2025

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