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Chlorine in PDB 6c7d: Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-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-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7d 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) 65.84 / 1.79
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.914, 73.703, 91.108, 109.56, 91.24, 91.03
R / Rfree (%) 18.7 / 23.2

Other elements in 6c7d:

The structure of Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide (pdb code 6c7d). 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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7d:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6c7d

Go back to Chlorine Binding Sites List in 6c7d
Chlorine binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2001

b:28.1
occ:1.00
 CL3 A:EOJ2001 0.0 28.1 1.0
C31 A:EOJ2001 1.7 18.2 1.0
C30 A:EOJ2001 2.7 21.3 1.0
C26 A:EOJ2001 2.7 20.9 1.0
C25 A:EOJ2001 3.1 23.6 1.0
C15 A:EOJ2001 3.3 24.7 1.0
N21 A:EOJ2001 3.3 24.4 1.0
C14 A:EOJ2001 3.4 24.4 1.0
CZ A:PHE830 3.5 23.3 1.0
CD1 A:ILE826 3.6 24.1 1.0
CE1 A:PHE830 3.7 23.5 1.0
O A:HOH2301 3.9 22.0 1.0
CE1 A:HIS656 3.9 16.1 1.0
N24 A:EOJ2001 3.9 25.6 1.0
C29 A:EOJ2001 4.0 20.7 1.0
C27 A:EOJ2001 4.0 27.1 1.0
O A:HOH2134 4.1 31.3 1.0
C16 A:EOJ2001 4.2 31.1 1.0
C20 A:EOJ2001 4.2 23.3 1.0
NE2 A:HIS656 4.3 19.8 1.0
O33 A:EOJ2001 4.3 30.9 1.0
C13 A:EOJ2001 4.5 27.2 1.0
C28 A:EOJ2001 4.5 23.5 1.0
N23 A:EOJ2001 4.6 26.5 1.0
C22 A:EOJ2001 4.7 32.2 1.0
CE2 A:PHE830 4.7 30.5 1.0
CG2 A:ILE826 4.8 28.1 1.0
CG1 A:ILE826 4.9 22.8 1.0

Chlorine binding site 2 out of 4 in 6c7d

Go back to Chlorine Binding Sites List in 6c7d
Chlorine binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2001

b:31.7
occ:1.00
 CL3 B:EOJ2001 0.0 31.7 1.0
C31 B:EOJ2001 1.7 29.0 1.0
C30 B:EOJ2001 2.7 27.0 1.0
C26 B:EOJ2001 2.7 32.3 1.0
C25 B:EOJ2001 3.0 32.6 1.0
N21 B:EOJ2001 3.3 22.2 1.0
C15 B:EOJ2001 3.4 27.9 1.0
C14 B:EOJ2001 3.5 25.6 1.0
CD1 B:ILE826 3.6 34.1 1.0
CZ B:PHE830 3.7 21.8 1.0
CE1 B:HIS656 3.7 17.7 1.0
O B:HOH2262 3.8 24.3 1.0
CE1 B:PHE830 3.8 24.2 1.0
N24 B:EOJ2001 3.9 36.6 1.0
C29 B:EOJ2001 3.9 23.8 1.0
C27 B:EOJ2001 4.0 28.8 1.0
NE2 B:HIS656 4.2 21.3 1.0
C20 B:EOJ2001 4.2 33.5 1.0
O B:HOH2194 4.3 35.0 1.0
C16 B:EOJ2001 4.3 30.4 1.0
O33 B:EOJ2001 4.4 31.2 1.0
C28 B:EOJ2001 4.5 27.1 1.0
N23 B:EOJ2001 4.5 37.7 1.0
C13 B:EOJ2001 4.6 25.8 1.0
ND1 B:HIS656 4.9 17.1 1.0
C22 B:EOJ2001 4.9 34.4 1.0
CG2 B:ILE826 4.9 23.5 1.0
CE2 B:PHE830 4.9 28.0 1.0
O B:HOH2180 5.0 15.2 1.0

Chlorine binding site 3 out of 4 in 6c7d

Go back to Chlorine Binding Sites List in 6c7d
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2001

b:82.7
occ:1.00
 CL3 C:EOJ2001 0.0 82.7 1.0
C31 C:EOJ2001 1.7 30.4 1.0
C26 C:EOJ2001 2.7 31.9 1.0
C30 C:EOJ2001 2.7 20.9 1.0
C25 C:EOJ2001 2.9 29.6 1.0
N21 C:EOJ2001 3.2 29.9 1.0
C15 C:EOJ2001 3.2 25.6 1.0
C14 C:EOJ2001 3.3 27.7 1.0
CZ C:PHE830 3.4 23.0 1.0
CE1 C:PHE830 3.7 28.9 1.0
CD1 C:ILE826 3.7 27.3 1.0
O C:HOH2214 3.8 26.0 1.0
N24 C:EOJ2001 3.8 29.8 1.0
C29 C:EOJ2001 3.9 24.3 1.0
C27 C:EOJ2001 4.0 33.5 1.0
CE1 C:HIS656 4.1 19.6 1.0
C20 C:EOJ2001 4.1 26.5 1.0
C16 C:EOJ2001 4.2 23.3 1.0
O33 C:EOJ2001 4.4 33.7 1.0
C13 C:EOJ2001 4.4 29.4 1.0
C28 C:EOJ2001 4.4 30.1 1.0
N23 C:EOJ2001 4.5 25.9 1.0
NE2 C:HIS656 4.6 21.0 1.0
CE2 C:PHE830 4.6 25.2 1.0
C22 C:EOJ2001 4.8 35.0 1.0
CD1 C:PHE830 5.0 23.1 1.0

Chlorine binding site 4 out of 4 in 6c7d

Go back to Chlorine Binding Sites List in 6c7d
Chlorine binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with N-(1-Adamantyl)- 1-(2-Chlorophenyl)-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-Chlorophenyl)-4-Methyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2001

b:82.1
occ:1.00
 CL3 D:EOJ2001 0.0 82.1 1.0
C31 D:EOJ2001 1.7 31.9 1.0
C30 D:EOJ2001 2.7 28.7 1.0
C26 D:EOJ2001 2.7 26.9 1.0
C25 D:EOJ2001 3.0 21.6 1.0
C15 D:EOJ2001 3.2 21.7 1.0
N21 D:EOJ2001 3.2 24.0 1.0
C14 D:EOJ2001 3.4 25.4 1.0
CZ D:PHE830 3.4 23.2 1.0
O D:HOH2153 3.6 35.0 1.0
CE1 D:PHE830 3.7 22.1 1.0
O D:HOH2254 3.8 27.6 1.0
N24 D:EOJ2001 3.9 25.7 1.0
C29 D:EOJ2001 3.9 28.8 1.0
CD1 D:ILE826 3.9 29.9 1.0
C27 D:EOJ2001 4.0 28.0 1.0
C16 D:EOJ2001 4.1 22.5 1.0
CE1 D:HIS656 4.1 16.0 1.0
C20 D:EOJ2001 4.2 24.4 1.0
O33 D:EOJ2001 4.3 25.8 1.0
C13 D:EOJ2001 4.4 22.9 1.0
C28 D:EOJ2001 4.4 23.4 1.0
N23 D:EOJ2001 4.5 25.5 1.0
NE2 D:HIS656 4.6 18.8 1.0
CE2 D:PHE830 4.6 29.0 1.0
C22 D:EOJ2001 4.7 24.2 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: Sat Jul 12 12:15:53 2025

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