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Chlorine in PDB 7g5k: Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm, PDB code: 7g5k was solved by M.Stihle, J.Benz, D.Hunziker, W.Harris, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.63 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.894, 91.268, 118.803, 90, 90, 90
R / Rfree (%) 18.1 / 21.8

Other elements in 7g5k:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Calcium (Ca) 1 atom
Potassium (K) 1 atom
Zinc (Zn) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm (pdb code 7g5k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm, PDB code: 7g5k:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7g5k

Go back to Chlorine Binding Sites List in 7g5k
Chlorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:46.2
occ:1.00
 CL11 A:Y1U901 0.0 46.2 1.0
C5 A:Y1U901 1.7 39.7 1.0
C2 A:Y1U901 2.7 38.0 1.0
C10 A:Y1U901 2.7 42.1 1.0
N1 A:Y1U901 2.9 36.1 1.0
C4 A:Y1U901 3.4 34.9 1.0
C3 A:Y1U901 3.6 33.9 1.0
CZ A:PHE210 3.6 38.5 1.0
O9 A:Y1U901 3.6 32.3 1.0
CE A:LYS248 3.6 49.4 1.0
C6 A:Y1U901 4.0 39.7 1.0
NZ A:LYS248 4.0 51.6 1.0
C17 A:Y1U901 4.0 39.1 1.0
CE2 A:PHE274 4.1 54.4 1.0
O A:LEU243 4.1 62.3 1.0
CZ A:PHE274 4.2 53.1 1.0
CE1 A:PHE210 4.3 39.2 1.0
N8 A:Y1U901 4.3 34.7 1.0
C7 A:Y1U901 4.4 34.2 1.0
CD A:LYS248 4.5 48.8 1.0
C12 A:Y1U901 4.5 39.1 1.0
CE2 A:PHE210 4.6 41.2 1.0
C14 A:Y1U901 4.7 34.3 1.0

Chlorine binding site 2 out of 3 in 7g5k

Go back to Chlorine Binding Sites List in 7g5k
Chlorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:49.2
occ:1.00
 CL13 A:Y1U901 0.0 49.2 1.0
C6 A:Y1U901 1.7 39.7 1.0
C2 A:Y1U901 2.7 38.0 1.0
C12 A:Y1U901 2.7 39.1 1.0
N1 A:Y1U901 2.9 36.1 1.0
O A:HOH1007 3.1 41.8 1.0
CG A:GLU308 3.3 25.6 0.5
C3 A:Y1U901 3.5 33.9 1.0
CG1 A:VAL277 3.5 42.7 1.0
C4 A:Y1U901 3.6 34.9 1.0
O9 A:Y1U901 3.9 32.3 1.0
C5 A:Y1U901 4.0 39.7 1.0
O A:HOH1066 4.0 40.8 1.0
CB A:GLU308 4.0 28.8 0.5
C17 A:Y1U901 4.0 39.1 1.0
CB A:GLU308 4.2 25.2 0.5
CD A:GLU308 4.4 25.3 0.5
OE2 A:GLU308 4.4 25.1 0.5
CG A:GLU308 4.5 32.0 0.5
CE2 A:TYR306 4.5 26.9 1.0
C7 A:Y1U901 4.5 34.2 1.0
C10 A:Y1U901 4.5 42.1 1.0
N8 A:Y1U901 4.6 34.7 1.0
CB A:VAL277 4.7 43.6 1.0
OH A:TYR306 4.8 31.8 1.0
O A:HOH1281 4.9 41.1 1.0
C14 A:Y1U901 5.0 34.3 1.0

Chlorine binding site 3 out of 3 in 7g5k

Go back to Chlorine Binding Sites List in 7g5k
Chlorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Rat Autotaxin in Complex with 3-(2,6- Dichlorophenyl)-7-[(2-Hydroxy-2-Phenylethyl)Amino]-1-Methyl-4H- Pyrimido[4,5-D]Pyrimidin-2-One, I.E. Smiles N1(C2C(CCCC2CL)Cl) CC2C(N(C1=O)C)Nc(NC2)Nc[C@@H](C1CCCCC1)O with IC50=0.0487403 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl906

b:43.0
occ:1.00
 O A:HOH1400 3.0 43.7 1.0
N A:ASN230 3.3 30.1 1.0
NH1 A:ARG391 3.5 24.3 1.0
CA A:GLY229 3.6 27.2 1.0
N A:SER231 3.7 32.0 1.0
C A:GLY229 3.9 28.1 1.0
O A:SER231 4.1 30.8 1.0
CG1 A:VAL385 4.2 30.5 1.0
CE A:LYS208 4.2 29.8 1.0
CA A:ASN230 4.2 32.1 1.0
CB A:ASN230 4.4 32.5 1.0
C A:ASN230 4.5 32.6 1.0
CG A:LYS208 4.5 24.4 1.0
CZ A:ARG391 4.5 24.2 1.0
CD1 A:LEU389 4.6 29.8 1.0
CD2 A:LEU389 4.6 31.6 1.0
CA A:SER231 4.6 32.5 1.0
CB A:SER231 4.7 38.3 1.0
O A:HOH1180 4.7 39.9 1.0
NH2 A:ARG391 4.7 24.8 1.0
C A:SER231 4.8 30.9 1.0
CG A:LEU389 4.8 28.0 1.0
N A:GLY229 5.0 22.7 1.0
CD A:LYS208 5.0 28.7 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: Sat Feb 8 17:01:13 2025

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