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Zinc 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
Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6c7f

Go back to Zinc Binding Sites List in 6c7f
Zinc 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 Zinc with other atoms in the Zn 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:Zn1002

b:20.6
occ:1.00
 NE2 A:HIS696 2.1 14.4 1.0
OD2 A:ASP697 2.1 16.3 1.0
OD1 A:ASP808 2.1 17.2 1.0
NE2 A:HIS660 2.2 16.1 1.0
O A:HOH1190 2.3 16.9 1.0
O A:HOH1112 2.4 20.8 1.0
CE1 A:HIS696 3.0 16.9 1.0
CG A:ASP808 3.0 16.9 1.0
CD2 A:HIS696 3.1 14.0 1.0
CE1 A:HIS660 3.1 13.4 1.0
CG A:ASP697 3.2 15.2 1.0
CD2 A:HIS660 3.2 19.6 1.0
OD2 A:ASP808 3.3 20.5 1.0
OD1 A:ASP697 3.7 16.4 1.0
O A:HOH1178 4.0 17.7 1.0
MG A:MG1003 4.0 18.3 1.0
ND1 A:HIS696 4.1 15.9 1.0
O A:HOH1216 4.2 14.8 1.0
CD2 A:HIS656 4.2 22.4 1.0
CG A:HIS696 4.2 12.3 1.0
ND1 A:HIS660 4.3 14.6 1.0
CB A:ASP697 4.3 16.6 1.0
CG A:HIS660 4.3 15.2 1.0
NE2 A:HIS656 4.4 17.7 1.0
CB A:ASP808 4.5 15.5 1.0
CG2 A:VAL664 4.8 14.0 1.0
CA A:ASP808 4.8 12.6 1.0
O A:HOH1133 4.8 13.7 1.0
O A:ASP808 5.0 21.4 1.0

Zinc binding site 2 out of 3 in 6c7f

Go back to Zinc Binding Sites List in 6c7f
Zinc 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 Zinc with other atoms in the Zn 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:Zn1002

b:21.5
occ:1.00
 OD2 B:ASP697 2.1 17.3 1.0
NE2 B:HIS660 2.1 18.6 1.0
OD1 B:ASP808 2.1 21.4 1.0
NE2 B:HIS696 2.1 15.2 1.0
O B:HOH1211 2.2 17.0 1.0
O B:HOH1117 2.5 19.2 1.0
CG B:ASP808 3.0 19.7 1.0
CE1 B:HIS660 3.0 17.4 1.0
CD2 B:HIS696 3.1 14.1 1.0
CE1 B:HIS696 3.1 18.8 1.0
CD2 B:HIS660 3.1 17.7 1.0
CG B:ASP697 3.1 16.8 1.0
OD2 B:ASP808 3.2 19.5 1.0
OD1 B:ASP697 3.7 14.7 1.0
MG B:MG1003 4.0 16.5 1.0
O B:HOH1158 4.0 19.8 1.0
ND1 B:HIS660 4.2 19.5 1.0
CD2 B:HIS656 4.2 19.8 1.0
O B:HOH1234 4.2 14.2 1.0
ND1 B:HIS696 4.2 16.6 1.0
CG B:HIS696 4.2 18.0 1.0
CG B:HIS660 4.2 16.4 1.0
CB B:ASP697 4.3 18.9 1.0
NE2 B:HIS656 4.4 19.7 1.0
CB B:ASP808 4.5 17.5 1.0
CA B:ASP808 4.9 17.9 1.0
CG2 B:VAL664 4.9 18.4 1.0
O B:HOH1120 4.9 16.0 1.0
O B:ASP808 5.0 19.1 1.0

Zinc binding site 3 out of 3 in 6c7f

Go back to Zinc Binding Sites List in 6c7f
Zinc 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 Zinc with other atoms in the Zn 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:Zn1002

b:23.2
occ:1.00
 OD2 C:ASP697 2.0 19.4 1.0
OD1 C:ASP808 2.1 21.4 1.0
NE2 C:HIS660 2.1 22.0 1.0
NE2 C:HIS696 2.2 17.7 1.0
O C:HOH1181 2.3 18.3 1.0
O C:HOH1126 2.6 19.0 1.0
CG C:ASP808 3.1 24.9 1.0
CD2 C:HIS696 3.1 18.0 1.0
CG C:ASP697 3.1 19.4 1.0
CE1 C:HIS660 3.1 20.1 1.0
CD2 C:HIS660 3.1 16.6 1.0
CE1 C:HIS696 3.2 17.6 1.0
OD2 C:ASP808 3.3 18.6 1.0
OD1 C:ASP697 3.6 20.0 1.0
O C:HOH1162 3.9 21.2 1.0
MG C:MG1003 4.0 18.0 1.0
O C:HOH1189 4.2 16.9 1.0
CD2 C:HIS656 4.2 20.6 1.0
ND1 C:HIS660 4.2 22.4 1.0
CG C:HIS696 4.2 16.9 1.0
CB C:ASP697 4.3 21.1 1.0
ND1 C:HIS696 4.3 16.6 1.0
CG C:HIS660 4.3 19.9 1.0
NE2 C:HIS656 4.3 23.1 1.0
CB C:ASP808 4.4 21.0 1.0
CA C:ASP808 4.8 23.2 1.0
O C:HOH1119 4.8 16.6 1.0
CG2 C:VAL664 4.9 18.1 1.0
O C:ASP808 4.9 23.2 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: Mon Oct 28 18:31:59 2024

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