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Chlorine in PDB 6c7f: Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7f 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) 71.73 / 1.82
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.248, 73.004, 91.953, 90.00, 110.33, 90.00
R / Rfree (%) 19.5 / 24.6

Other elements in 6c7f:

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

Magnesium (Mg) 3 atoms
Zinc (Zn) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide (pdb code 6c7f). 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 Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-N,4-Dimethyl-[1,2,4]Triazolo[4,3-A]Quinoxaline-8- Carboxamide, PDB code: 6c7f:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6c7f

Go back to Chlorine Binding Sites List in 6c7f
Chlorine binding site 1 out of 3 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-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:27.7
occ:1.00
 CL3 A:EOS1001 0.0 27.7 1.0
C22 A:EOS1001 1.7 21.9 1.0
C21 A:EOS1001 2.6 28.8 1.0
C17 A:EOS1001 2.7 22.8 1.0
C16 A:EOS1001 3.0 20.8 1.0
N10 A:EOS1001 3.3 17.7 1.0
C4 A:EOS1001 3.4 20.1 1.0
C3 A:EOS1001 3.5 20.0 1.0
CZ A:PHE830 3.6 17.7 1.0
CD1 A:ILE826 3.8 31.4 1.0
CE1 A:HIS656 3.8 19.8 1.0
CE1 A:PHE830 3.8 26.2 1.0
N15 A:EOS1001 3.8 19.2 1.0
C20 A:EOS1001 3.9 24.2 1.0
C18 A:EOS1001 4.0 23.2 1.0
O A:HOH1300 4.1 22.0 1.0
C9 A:EOS1001 4.2 21.8 1.0
NE2 A:HIS656 4.2 17.7 1.0
C5 A:EOS1001 4.3 29.4 1.0
O A:HOH1104 4.4 30.5 1.0
C19 A:EOS1001 4.4 29.9 1.0
N14 A:EOS1001 4.5 22.6 1.0
C2 A:EOS1001 4.5 24.1 1.0
O13 A:EOS1001 4.5 33.4 1.0
CG2 A:ILE826 4.5 20.3 1.0
CG1 A:ILE826 4.7 23.8 1.0
CE2 A:PHE830 4.7 24.0 1.0
CD2 A:TYR655 4.8 18.0 1.0
CE2 A:TYR655 4.8 18.6 1.0
C11 A:EOS1001 4.9 32.1 1.0
ND1 A:HIS656 4.9 18.1 1.0

Chlorine binding site 2 out of 3 in 6c7f

Go back to Chlorine Binding Sites List in 6c7f
Chlorine binding site 2 out of 3 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-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:27.9
occ:1.00
 CL3 B:EOS1001 0.0 27.9 1.0
C22 B:EOS1001 1.7 28.1 1.0
C21 B:EOS1001 2.7 28.0 1.0
C17 B:EOS1001 2.7 22.8 1.0
C16 B:EOS1001 3.1 27.2 1.0
N10 B:EOS1001 3.4 25.4 1.0
C4 B:EOS1001 3.5 15.9 1.0
CZ B:PHE830 3.6 21.8 1.0
C3 B:EOS1001 3.6 24.4 1.0
O B:HOH1110 3.7 27.7 1.0
CD1 B:ILE826 3.7 23.3 1.0
CE1 B:HIS656 3.8 20.0 1.0
CE1 B:PHE830 3.8 23.7 1.0
N15 B:EOS1001 3.9 20.9 1.0
C20 B:EOS1001 4.0 25.8 1.0
O B:HOH1283 4.0 22.4 1.0
C18 B:EOS1001 4.0 17.8 1.0
NE2 B:HIS656 4.2 19.7 1.0
C9 B:EOS1001 4.3 26.4 1.0
O13 B:EOS1001 4.4 23.9 1.0
C5 B:EOS1001 4.4 22.1 1.0
C19 B:EOS1001 4.5 30.8 1.0
N14 B:EOS1001 4.6 27.1 1.0
C2 B:EOS1001 4.7 23.3 1.0
CE2 B:PHE830 4.8 24.5 1.0
O B:HOH1219 4.9 22.9 1.0
C11 B:EOS1001 4.9 21.3 1.0
ND1 B:HIS656 4.9 18.4 1.0

Chlorine binding site 3 out of 3 in 6c7f

Go back to Chlorine Binding Sites List in 6c7f
Chlorine binding site 3 out of 3 in the Crystal Structure of Human Phosphodiesterase 2A with 1-(2-Chloro-5- Isobutoxy-Phenyl)-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-Chloro-5- Isobutoxy-Phenyl)-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:29.5
occ:1.00
 CL3 C:EOS1001 0.0 29.5 1.0
C22 C:EOS1001 1.7 27.9 1.0
C21 C:EOS1001 2.7 34.7 1.0
C17 C:EOS1001 2.7 26.1 1.0
C16 C:EOS1001 3.0 26.7 1.0
N10 C:EOS1001 3.2 22.9 1.0
C4 C:EOS1001 3.3 22.8 1.0
C3 C:EOS1001 3.4 25.1 1.0
CZ C:PHE830 3.4 27.6 1.0
CE1 C:PHE830 3.8 26.9 1.0
N15 C:EOS1001 3.8 27.5 1.0
CE1 C:HIS656 3.9 17.7 1.0
C20 C:EOS1001 3.9 34.1 1.0
O C:HOH1198 3.9 40.1 1.0
C18 C:EOS1001 4.0 26.2 1.0
C9 C:EOS1001 4.1 28.7 1.0
O C:HOH1253 4.1 33.4 1.0
C5 C:EOS1001 4.3 26.1 1.0
NE2 C:HIS656 4.4 23.1 1.0
C2 C:EOS1001 4.4 26.1 1.0
N14 C:EOS1001 4.4 28.4 1.0
C19 C:EOS1001 4.5 28.8 1.0
O13 C:EOS1001 4.5 29.7 1.0
CE2 C:PHE830 4.6 27.3 1.0
CG2 C:ILE826 4.7 25.8 1.0
CG1 C:ILE826 4.8 27.3 1.0
CD1 C:ILE826 4.8 36.7 1.0
C11 C:EOS1001 4.9 32.5 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 23:19:13 2024

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