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Chlorine in PDB 7g4k: Crystal Structure of Rat Autotaxin in Complex with 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 Microm, PDB code: 7g4k was solved by M.Stihle, J.Benz, D.Hunziker, R.Goodnow, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.67 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.91, 91.348, 120.108, 90, 90, 90
R / Rfree (%) 19.7 / 24.2

Other elements in 7g4k:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Sodium (Na) 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 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 Microm (pdb code 7g4k). 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 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 Microm, PDB code: 7g4k:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7g4k

Go back to Chlorine Binding Sites List in 7g4k
Chlorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 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 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:19.9
occ:0.70
 CL26 A:XJK901 0.0 19.9 0.7
CL26 A:XJK901 1.2 20.2 0.3
C21 A:XJK901 1.7 22.7 0.7
C21 A:XJK901 2.1 19.4 0.3
C24 A:XJK901 2.7 19.7 0.7
C25 A:XJK901 2.7 22.2 0.7
C24 A:XJK901 3.0 18.3 0.3
C25 A:XJK901 3.0 19.6 0.3
CE A:MET512 3.4 16.7 1.0
CA A:ALA217 3.7 11.2 1.0
CD2 A:LEU259 3.7 15.5 1.0
SD A:MET512 3.9 17.6 1.0
CD1 A:ILE167 4.0 20.1 1.0
C19 A:XJK901 4.0 20.6 0.7
CB A:LEU259 4.0 14.9 1.0
O A:LEU216 4.0 11.7 1.0
C20 A:XJK901 4.1 22.9 0.7
CE2 A:PHE273 4.1 24.4 1.0
CG A:LEU216 4.1 19.0 1.0
C19 A:XJK901 4.2 18.2 0.3
N A:ALA217 4.2 12.2 1.0
C20 A:XJK901 4.2 18.5 0.3
C A:LEU216 4.3 12.4 1.0
CB A:ALA217 4.4 11.4 1.0
CD2 A:LEU216 4.4 17.7 1.0
C16 A:XJK901 4.5 22.0 0.7
CG A:LEU259 4.5 17.0 1.0
CD2 A:PHE273 4.7 23.5 1.0
C16 A:XJK901 4.7 18.6 0.3
C A:ALA217 4.7 11.9 1.0
O A:ALA217 4.8 12.3 1.0
CB A:LEU216 5.0 13.9 1.0
C27 A:XJK901 5.0 18.3 0.3
CD1 A:LEU216 5.0 19.8 1.0
CG1 A:ILE167 5.0 17.1 1.0

Chlorine binding site 2 out of 3 in 7g4k

Go back to Chlorine Binding Sites List in 7g4k
Chlorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 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 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:20.2
occ:0.30
 CL26 A:XJK901 0.0 20.2 0.3
CL26 A:XJK901 1.2 19.9 0.7
C21 A:XJK901 1.6 22.7 0.7
C21 A:XJK901 1.7 19.4 0.3
C25 A:XJK901 2.1 22.2 0.7
C25 A:XJK901 2.7 19.6 0.3
C24 A:XJK901 2.7 18.3 0.3
C24 A:XJK901 2.7 19.7 0.7
CD1 A:ILE167 3.4 20.1 1.0
C20 A:XJK901 3.4 22.9 0.7
CE A:MET512 3.5 16.7 1.0
SD A:MET512 3.6 17.6 1.0
CG A:LEU216 3.6 19.0 1.0
CD2 A:LEU216 3.6 17.7 1.0
C19 A:XJK901 3.8 20.6 0.7
CG2 A:ILE167 3.9 16.1 1.0
C20 A:XJK901 4.0 18.5 0.3
C19 A:XJK901 4.0 18.2 0.3
C16 A:XJK901 4.1 22.0 0.7
CG1 A:ILE167 4.1 17.1 1.0
CD2 A:LEU259 4.4 15.5 1.0
CB A:ILE167 4.4 15.9 1.0
CD1 A:LEU216 4.4 19.8 1.0
CE2 A:PHE273 4.5 24.4 1.0
O A:LEU216 4.5 11.7 1.0
C16 A:XJK901 4.5 18.6 0.3
CA A:ALA217 4.6 11.2 1.0
C A:LEU216 4.6 12.4 1.0
CB A:LEU216 4.7 13.9 1.0
N A:ALA217 4.8 12.2 1.0
CD2 A:PHE273 5.0 23.5 1.0

Chlorine binding site 3 out of 3 in 7g4k

Go back to Chlorine Binding Sites List in 7g4k
Chlorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 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 5-(4-Chlorophenyl)- 2-(5,6-Dimethoxybenzimidazol-1-Yl)-N-Methyl-1,3-Thiazole-4- Carboxamide, I.E. Smiles C1(=Nc(=C(S1)C1CCC(CC1)Cl)C(=O)Nc) N1C2C(N=C1)Cc(C(C2)Oc)Oc with IC50=0.0108616 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl905

b:35.0
occ:1.00
 N A:ASN230 3.2 23.0 1.0
NH1 A:ARG391 3.3 22.9 1.0
NZ A:LYS208 3.4 36.2 1.0
CA A:GLY229 3.5 17.3 1.0
N A:SER231 3.7 29.3 1.0
C A:GLY229 3.8 18.7 1.0
CG1 A:VAL385 4.1 24.0 1.0
O A:SER231 4.1 25.1 1.0
CA A:ASN230 4.2 24.1 1.0
CZ A:ARG391 4.4 23.6 1.0
CB A:ASN230 4.4 25.9 1.0
C A:ASN230 4.4 29.2 1.0
CD1 A:LEU389 4.4 22.6 1.0
CB A:SER231 4.5 32.2 1.0
O A:HOH1129 4.6 32.9 1.0
NH2 A:ARG391 4.6 23.0 1.0
CA A:SER231 4.6 28.3 1.0
CG A:LYS208 4.6 21.1 1.0
CE A:LYS208 4.8 30.6 1.0
CG A:LEU389 4.8 22.2 1.0
C A:SER231 4.8 25.4 1.0
N A:GLY229 4.8 14.7 1.0
O A:GLY229 4.9 17.8 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 16:57:04 2025

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