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Zinc in PDB 7g3t: Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm, PDB code: 7g3t was solved by M.Stihle, J.Benz, D.Hunziker, E.Pinard, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.92 / 1.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.77, 91.69, 120.29, 90, 90, 90
R / Rfree (%) 13.5 / 17.2

Other elements in 7g3t:

The structure of Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm (pdb code 7g3t). 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 (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm, PDB code: 7g3t:

Zinc binding site 1 out of 1 in 7g3t

Go back to Zinc Binding Sites List in 7g3t
Zinc binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 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 (2S)-6-Chloro-2- [[5-(6-Oxa-1-Azaspiro[3.3]Heptane-1-Carbonyl)Pyrimidin-2-Yl]Amino]-2, 3-Dihydro-1H-Indene-4-Carbonitrile, I.E. Smiles C1C2CC(Cc(C#N) C2C[C@H]1NC1NCC(CN1)C(=O)N1C2(COC2)CC1)Cl with IC50=0.00758135 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:13.6
occ:1.00
 O A:ACT908 1.9 21.8 1.0
NE2 A:HIS315 2.0 12.4 1.0
NE2 A:HIS474 2.1 11.5 1.0
OD1 A:ASP311 2.2 19.4 1.0
OD2 A:ASP311 2.5 19.6 1.0
CG A:ASP311 2.7 15.0 1.0
C A:ACT908 2.8 34.4 1.0
CE1 A:HIS315 3.0 15.9 1.0
CD2 A:HIS315 3.0 13.4 1.0
CD2 A:HIS474 3.0 12.2 1.0
CE1 A:HIS474 3.1 12.0 1.0
OXT A:ACT908 3.1 46.7 1.0
O A:HOH1118 3.8 22.7 1.0
ND1 A:HIS315 4.1 17.1 1.0
CG A:HIS315 4.1 13.4 1.0
CB A:ASP311 4.2 12.1 1.0
ND1 A:HIS474 4.2 11.9 1.0
CG A:HIS474 4.2 11.8 1.0
CH3 A:ACT908 4.2 29.7 1.0
CE1 A:HIS359 4.2 13.3 1.0
OG1 A:THR209 4.3 14.4 1.0
O A:HOH1003 4.4 8.8 0.5
CE A:MET361 4.5 14.0 1.0
NE2 A:HIS359 4.5 12.5 1.0
CA A:CA906 4.5 36.2 1.0
O A:HOH1032 4.7 48.7 1.0
OD2 A:ASP171 4.8 21.2 1.0
O A:ASP311 4.9 13.3 1.0
OD1 A:ASP171 4.9 16.7 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 00:24:08 2025

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