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Chlorine in PDB 6c7e: Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[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 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7e 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) 34.31 / 1.43
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.960, 72.650, 90.730, 109.11, 91.28, 91.20
R / Rfree (%) 17.4 / 20.1

Other elements in 6c7e:

The structure of Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[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 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide (pdb code 6c7e). 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 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7e:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6c7e

Go back to Chlorine Binding Sites List in 6c7e
Chlorine binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[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 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1001

b:16.8
occ:1.00
 CL3 A:EOG1001 0.0 16.8 1.0
C22 A:EOG1001 1.7 12.7 1.0
C21 A:EOG1001 2.6 17.2 1.0
C17 A:EOG1001 2.7 14.0 1.0
C16 A:EOG1001 3.0 14.4 1.0
N13 A:EOG1001 3.3 14.7 1.0
C6 A:EOG1001 3.3 15.0 1.0
C5 A:EOG1001 3.5 13.1 1.0
CZ A:PHE830 3.6 14.1 1.0
CE1 A:PHE830 3.7 17.4 1.0
CE1 A:HIS656 3.8 12.6 1.0
N15 A:EOG1001 3.9 14.7 1.0
C20 A:EOG1001 3.9 16.9 1.0
O A:HOH1413 4.0 15.9 1.0
C18 A:EOG1001 4.0 16.0 1.0
C12 A:EOG1001 4.2 18.4 1.0
C1 A:EOG1001 4.3 14.5 1.0
NE2 A:HIS656 4.3 14.8 1.0
O A:HOH1156 4.4 27.3 1.0
O9 A:EOG1001 4.4 25.4 1.0
CG2 A:ILE826 4.4 22.2 1.0
C19 A:EOG1001 4.5 14.8 1.0
C4 A:EOG1001 4.5 15.0 1.0
N14 A:EOG1001 4.6 20.8 1.0
C7 A:EOG1001 4.8 25.9 1.0
CD1 A:ILE826 4.8 31.3 1.0
CE2 A:PHE830 4.8 18.6 1.0
CG1 A:ILE826 4.8 18.7 1.0
ND1 A:HIS656 5.0 12.7 1.0
CD1 A:PHE830 5.0 13.2 1.0

Chlorine binding site 2 out of 4 in 6c7e

Go back to Chlorine Binding Sites List in 6c7e
Chlorine binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[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 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1001

b:18.1
occ:1.00
 CL3 B:EOG1001 0.0 18.1 1.0
C22 B:EOG1001 1.7 15.2 1.0
C21 B:EOG1001 2.7 19.3 1.0
C17 B:EOG1001 2.7 14.7 1.0
C16 B:EOG1001 3.1 13.8 1.0
N13 B:EOG1001 3.3 16.6 1.0
C6 B:EOG1001 3.4 15.4 1.0
C5 B:EOG1001 3.5 13.8 1.0
CZ B:PHE830 3.7 15.3 1.0
CE1 B:HIS656 3.8 12.6 1.0
CE1 B:PHE830 3.8 17.3 1.0
N15 B:EOG1001 3.9 16.7 1.0
C20 B:EOG1001 4.0 14.1 1.0
C18 B:EOG1001 4.0 16.2 1.0
O B:HOH1398 4.1 18.4 1.0
C12 B:EOG1001 4.2 18.2 1.0
NE2 B:HIS656 4.2 13.7 1.0
O B:HOH1146 4.3 24.9 1.0
C1 B:EOG1001 4.3 16.8 1.0
CG2 B:ILE826 4.3 21.1 1.0
CD1 B:ILE826 4.4 23.4 1.0
O9 B:EOG1001 4.5 23.0 1.0
C19 B:EOG1001 4.5 14.1 1.0
C4 B:EOG1001 4.5 16.7 1.0
N14 B:EOG1001 4.5 18.1 1.0
CG1 B:ILE826 4.7 18.8 1.0
CE2 B:TYR655 4.8 16.2 1.0
CD2 B:TYR655 4.9 14.4 1.0
C7 B:EOG1001 4.9 22.6 1.0
CE2 B:PHE830 4.9 19.3 1.0
ND1 B:HIS656 4.9 13.7 1.0

Chlorine binding site 3 out of 4 in 6c7e

Go back to Chlorine Binding Sites List in 6c7e
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[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 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1001

b:20.1
occ:1.00
 CL3 C:EOG1001 0.0 20.1 1.0
C22 C:EOG1001 1.7 15.1 1.0
C21 C:EOG1001 2.7 14.8 1.0
C17 C:EOG1001 2.7 14.2 1.0
C16 C:EOG1001 3.0 16.1 1.0
N13 C:EOG1001 3.3 18.0 1.0
C6 C:EOG1001 3.3 17.4 1.0
C5 C:EOG1001 3.5 17.4 1.0
CD1 C:ILE826 3.5 21.1 1.0
CZ C:PHE830 3.6 18.8 1.0
CE1 C:PHE830 3.7 19.8 1.0
CE1 C:HIS656 3.8 15.8 1.0
N15 C:EOG1001 3.9 20.7 1.0
C20 C:EOG1001 3.9 18.9 1.0
C18 C:EOG1001 4.0 14.5 1.0
O C:HOH1104 4.0 27.4 1.0
O C:HOH1336 4.1 17.0 1.0
C12 C:EOG1001 4.2 20.1 1.0
C1 C:EOG1001 4.3 16.9 1.0
NE2 C:HIS656 4.3 16.2 1.0
O9 C:EOG1001 4.4 27.0 1.0
C19 C:EOG1001 4.4 20.1 1.0
C4 C:EOG1001 4.5 18.2 1.0
N14 C:EOG1001 4.5 19.3 1.0
CG2 C:ILE826 4.7 23.9 1.0
C7 C:EOG1001 4.8 28.5 1.0
O C:HOH1174 4.9 18.4 1.0
CE2 C:PHE830 4.9 18.3 1.0
ND1 C:HIS656 4.9 14.8 1.0
CG1 C:ILE826 4.9 20.6 1.0

Chlorine binding site 4 out of 4 in 6c7e

Go back to Chlorine Binding Sites List in 6c7e
Chlorine binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2- Chlorophenyl)-N,4-Dimethyl-[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 1-(2- Chlorophenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1001

b:17.9
occ:1.00
 CL3 D:EOG1001 0.0 17.9 1.0
C22 D:EOG1001 1.7 12.9 1.0
C21 D:EOG1001 2.7 14.9 1.0
C17 D:EOG1001 2.7 14.5 1.0
C16 D:EOG1001 3.0 14.5 1.0
N13 D:EOG1001 3.3 15.4 1.0
C6 D:EOG1001 3.4 15.1 1.0
C5 D:EOG1001 3.5 15.8 1.0
CZ D:PHE830 3.6 13.4 1.0
CE1 D:PHE830 3.7 14.9 1.0
CE1 D:HIS656 3.8 12.7 1.0
N15 D:EOG1001 3.8 18.4 1.0
C20 D:EOG1001 3.9 16.1 1.0
C18 D:EOG1001 4.0 15.1 1.0
O D:HOH1358 4.1 17.4 1.0
C12 D:EOG1001 4.2 18.3 1.0
O D:HOH1137 4.2 24.3 1.0
C1 D:EOG1001 4.3 14.3 1.0
NE2 D:HIS656 4.4 13.2 1.0
O9 D:EOG1001 4.4 21.2 1.0
CG2 D:ILE826 4.4 20.7 1.0
C19 D:EOG1001 4.4 14.3 1.0
N14 D:EOG1001 4.5 21.9 1.0
C4 D:EOG1001 4.5 15.7 1.0
CG1 D:ILE826 4.8 20.0 1.0
CE2 D:PHE830 4.8 18.3 1.0
CD1 D:ILE826 4.8 27.2 1.0
C7 D:EOG1001 4.9 20.4 1.0
ND1 D:HIS656 4.9 13.6 1.0
CD1 D:PHE830 5.0 15.5 1.0
CE2 D:TYR655 5.0 14.0 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 23:19:09 2024

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