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Zinc in PDB 7g7d: Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm, PDB code: 7g7d 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) 45.71 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.702, 91.424, 118.999, 90, 90, 90
R / Rfree (%) 18.9 / 23.7

Other elements in 7g7d:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Potassium (K) 1 atom
Calcium (Ca) 1 atom
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm (pdb code 7g7d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm, PDB code: 7g7d:

Zinc binding site 1 out of 1 in 7g7d

Go back to Zinc Binding Sites List in 7g7d
Zinc binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 5-[3-Oxo-3-[Rac- (3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]- 1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2-Yl]Propyl]-3H-1,3- Oxazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)CCC1=Cnc(=O)O1 with IC50=0.0580555 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn906

b:36.8
occ:1.00
 N35 A:XLT901 1.7 53.4 0.5
N35 A:XLT901 1.8 53.5 0.5
NE2 A:HIS474 2.1 24.7 1.0
NE2 A:HIS315 2.1 36.3 1.0
OD1 A:ASP311 2.2 35.8 1.0
C34 A:XLT901 2.6 55.1 0.5
OD2 A:ASP311 2.6 40.2 1.0
C34 A:XLT901 2.7 55.6 0.5
CG A:ASP311 2.7 37.8 1.0
C36 A:XLT901 2.8 52.8 0.5
CD2 A:HIS315 3.0 29.5 1.0
C36 A:XLT901 3.0 53.9 0.5
CD2 A:HIS474 3.1 28.7 1.0
CE1 A:HIS474 3.1 25.9 1.0
CE1 A:HIS315 3.1 36.7 1.0
O38 A:XLT901 3.4 47.2 0.5
O38 A:XLT901 3.7 48.0 0.5
C33 A:XLT901 3.7 59.9 0.5
C33 A:XLT901 3.8 59.3 0.5
O37 A:XLT901 3.9 55.5 0.5
O37 A:XLT901 4.0 57.2 0.5
CG A:HIS315 4.2 32.4 1.0
ND1 A:HIS315 4.2 35.2 1.0
ND1 A:HIS474 4.2 26.4 1.0
CG A:HIS474 4.2 26.6 1.0
CB A:ASP311 4.2 34.6 1.0
CE1 A:HIS359 4.3 28.6 1.0
OG1 A:THR209 4.4 42.5 1.0
CE A:MET361 4.4 33.3 1.0
NE2 A:HIS359 4.6 32.9 1.0
OD1 A:ASP171 4.7 47.2 1.0
O A:ASP311 4.9 33.9 1.0
OD2 A:ASP171 5.0 55.9 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: Sun Feb 9 00:37:40 2025

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