Chlorine in PDB 6c7g: Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide, PDB code: 6c7g was solved by R.Xu, K.Aertgeerts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.13 / 1.68
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.141, 73.992, 91.743, 109.48, 91.49, 91.04
R / Rfree (%) 19.7 / 23.4

Other elements in 6c7g:

The structure of Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide (pdb code 6c7g). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide, PDB code: 6c7g:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6c7g

Go back to Chlorine Binding Sites List in 6c7g
Chlorine binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide


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 Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1001

b:23.9
occ:1.00
 CL3 A:EOY1001 0.0 23.9 1.0
C22 A:EOY1001 1.7 16.0 1.0
C21 A:EOY1001 2.6 18.4 1.0
C17 A:EOY1001 2.7 17.6 1.0
C16 A:EOY1001 3.1 15.2 1.0
CD1 A:ILE826 3.2 14.5 1.0
N10 A:EOY1001 3.4 10.5 1.0
C4 A:EOY1001 3.4 13.2 1.0
C3 A:EOY1001 3.6 16.0 1.0
CZ A:PHE830 3.6 19.0 1.0
CE1 A:PHE830 3.8 22.3 1.0
CE1 A:HIS656 3.8 9.9 1.0
C20 A:EOY1001 3.9 17.5 1.0
N15 A:EOY1001 3.9 13.2 1.0
C18 A:EOY1001 4.0 17.4 1.0
O A:HOH1304 4.1 16.1 1.0
O A:HOH1107 4.3 25.0 1.0
C9 A:EOY1001 4.3 15.0 1.0
C5 A:EOY1001 4.3 18.0 1.0
O13 A:EOY1001 4.4 29.1 1.0
NE2 A:HIS656 4.4 10.9 1.0
C19 A:EOY1001 4.5 22.4 1.0
CG2 A:ILE826 4.6 19.2 1.0
C2 A:EOY1001 4.6 18.2 1.0
N14 A:EOY1001 4.6 15.3 1.0
CG1 A:ILE826 4.6 15.1 1.0
CE2 A:PHE830 4.8 21.0 1.0
CD2 A:TYR655 4.8 10.9 1.0
CE2 A:TYR655 4.8 11.7 1.0
C11 A:EOY1001 4.9 23.7 1.0
ND1 A:HIS656 4.9 9.3 1.0

Chlorine binding site 2 out of 4 in 6c7g

Go back to Chlorine Binding Sites List in 6c7g
Chlorine binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide


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 Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1001

b:20.3
occ:1.00
 CL3 B:EOY1001 0.0 20.3 1.0
C22 B:EOY1001 1.7 13.0 1.0
C21 B:EOY1001 2.6 16.9 1.0
C17 B:EOY1001 2.8 12.5 1.0
C16 B:EOY1001 3.0 16.0 1.0
N10 B:EOY1001 3.3 15.1 1.0
C4 B:EOY1001 3.5 16.6 1.0
C3 B:EOY1001 3.5 16.6 1.0
CZ B:PHE830 3.6 20.8 1.0
CE1 B:PHE830 3.7 20.1 1.0
N15 B:EOY1001 3.8 19.8 1.0
CE1 B:HIS656 3.8 12.9 1.0
C20 B:EOY1001 3.9 11.8 1.0
C18 B:EOY1001 4.0 12.5 1.0
C9 B:EOY1001 4.1 19.2 1.0
O B:HOH1269 4.2 22.0 1.0
CD1 B:ILE826 4.3 25.3 1.0
CG2 B:ILE826 4.3 15.2 1.0
CG1 B:ILE826 4.4 19.2 1.0
NE2 B:HIS656 4.4 11.9 1.0
C5 B:EOY1001 4.4 19.8 1.0
N14 B:EOY1001 4.4 20.6 1.0
C19 B:EOY1001 4.5 18.1 1.0
C2 B:EOY1001 4.5 13.8 1.0
O13 B:EOY1001 4.6 22.7 1.0
O B:HOH1196 4.7 27.6 1.0
CD2 B:TYR655 4.8 13.0 1.0
CE2 B:TYR655 4.8 11.1 1.0
CE2 B:PHE830 4.8 16.0 1.0
ND1 B:HIS656 4.9 12.4 1.0
CD1 B:PHE830 5.0 14.9 1.0
C11 B:EOY1001 5.0 22.4 1.0
CB B:ILE826 5.0 17.7 1.0

Chlorine binding site 3 out of 4 in 6c7g

Go back to Chlorine Binding Sites List in 6c7g
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide


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 Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1001

b:21.3
occ:1.00
 CL3 C:EOY1001 0.0 21.3 1.0
C22 C:EOY1001 1.7 22.6 1.0
C21 C:EOY1001 2.6 24.1 1.0
C17 C:EOY1001 2.7 17.8 1.0
C16 C:EOY1001 3.1 13.4 1.0
N10 C:EOY1001 3.3 13.1 1.0
C4 C:EOY1001 3.4 16.7 1.0
C3 C:EOY1001 3.6 16.5 1.0
CD1 C:ILE826 3.6 19.2 1.0
CZ C:PHE830 3.6 16.1 1.0
CE1 C:PHE830 3.7 15.1 1.0
CE1 C:HIS656 3.8 8.1 1.0
C20 C:EOY1001 3.9 23.8 1.0
N15 C:EOY1001 3.9 13.5 1.0
C18 C:EOY1001 4.0 22.9 1.0
O C:HOH1107 4.1 26.7 1.0
O C:HOH1240 4.1 19.0 1.0
C9 C:EOY1001 4.2 15.9 1.0
C5 C:EOY1001 4.3 16.0 1.0
O13 C:EOY1001 4.4 28.3 1.0
NE2 C:HIS656 4.4 10.1 1.0
C19 C:EOY1001 4.5 28.2 1.0
N14 C:EOY1001 4.6 16.1 1.0
C2 C:EOY1001 4.6 17.2 1.0
CG2 C:ILE826 4.7 27.6 1.0
CE2 C:PHE830 4.8 15.7 1.0
C11 C:EOY1001 4.9 22.8 1.0
ND1 C:HIS656 4.9 10.4 1.0
CG1 C:ILE826 5.0 16.9 1.0
CD1 C:PHE830 5.0 16.0 1.0

Chlorine binding site 4 out of 4 in 6c7g

Go back to Chlorine Binding Sites List in 6c7g
Chlorine binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chloro-5-Isobutoxy-Phenyl)-4-Methyl-[1,2,4]Triazolo[4,3- A]Quinoxaline-8-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1001

b:24.4
occ:1.00
 CL3 D:EOY1001 0.0 24.4 1.0
C22 D:EOY1001 1.7 15.1 1.0
C21 D:EOY1001 2.7 19.0 1.0
C17 D:EOY1001 2.7 15.3 1.0
C16 D:EOY1001 3.0 15.6 1.0
C4 D:EOY1001 3.4 11.1 1.0
N10 D:EOY1001 3.4 15.7 1.0
C3 D:EOY1001 3.6 18.1 1.0
CZ D:PHE830 3.6 15.3 1.0
CE1 D:PHE830 3.7 14.5 1.0
CE1 D:HIS656 3.8 9.9 1.0
N15 D:EOY1001 3.9 15.6 1.0
C20 D:EOY1001 3.9 22.2 1.0
C18 D:EOY1001 4.0 21.4 1.0
O D:HOH1246 4.2 17.6 1.0
NE2 D:HIS656 4.2 13.6 1.0
C9 D:EOY1001 4.3 17.3 1.0
C5 D:EOY1001 4.3 11.8 1.0
CG2 D:ILE826 4.3 12.6 1.0
O13 D:EOY1001 4.4 17.4 1.0
C19 D:EOY1001 4.4 23.5 1.0
N14 D:EOY1001 4.6 17.7 1.0
C2 D:EOY1001 4.7 16.5 1.0
CD1 D:ILE826 4.8 23.5 1.0
CE2 D:PHE830 4.8 21.4 1.0
C11 D:EOY1001 4.9 16.2 1.0
CG1 D:ILE826 4.9 23.6 1.0
CE2 D:TYR655 4.9 11.7 1.0
CD2 D:TYR655 4.9 13.2 1.0
ND1 D:HIS656 5.0 11.9 1.0

Reference:

L.Gomez, R.Xu, W.Sinko, B.Selfridge, W.Vernier, K.Ly, R.Truong, M.Metz, T.Marrone, K.Sebring, Y.Yan, B.Appleton, K.Aertgeerts, M.E.Massari, J.G.Breitenbucher. Mathematical and Structural Characterization of Strong Nonadditive Structure-Activity Relationship Caused By Protein Conformational Changes. J. Med. Chem. V. 61 7754 2018.
ISSN: ISSN 1520-4804
PubMed: 30070482
DOI: 10.1021/ACS.JMEDCHEM.8B00713
Page generated: Fri Jul 26 23:21:34 2024

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