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Zinc 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
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6c7g

Go back to Zinc Binding Sites List in 6c7g
Zinc 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 Zinc with other atoms in the Zn 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:Zn1002

b:10.9
occ:1.00
 NE2 A:HIS660 2.1 6.5 1.0
NE2 A:HIS696 2.1 5.9 1.0
OD2 A:ASP697 2.1 7.5 1.0
OD1 A:ASP808 2.1 12.7 1.0
O A:HOH1197 2.2 8.0 1.0
O A:HOH1121 2.4 8.0 1.0
CE1 A:HIS660 3.0 8.1 1.0
CD2 A:HIS696 3.0 5.7 1.0
CG A:ASP808 3.1 10.6 1.0
CE1 A:HIS696 3.1 6.9 1.0
CD2 A:HIS660 3.1 11.9 1.0
CG A:ASP697 3.2 6.6 1.0
OD2 A:ASP808 3.3 11.5 1.0
OD1 A:ASP697 3.7 8.4 1.0
O A:HOH1158 4.0 9.9 1.0
MG A:MG1003 4.0 7.8 1.0
ND1 A:HIS660 4.1 8.7 1.0
CD2 A:HIS656 4.1 9.3 1.0
ND1 A:HIS696 4.2 6.8 1.0
CG A:HIS696 4.2 6.1 1.0
CG A:HIS660 4.2 10.3 1.0
NE2 A:HIS656 4.2 10.9 1.0
O A:HOH1161 4.2 7.2 1.0
CB A:ASP697 4.3 10.2 1.0
CB A:ASP808 4.5 9.0 1.0
O A:HOH1128 4.8 6.3 1.0
CG2 A:VAL664 4.8 6.6 1.0
CA A:ASP808 4.9 8.3 1.0
O A:ASP808 4.9 9.7 1.0

Zinc binding site 2 out of 4 in 6c7g

Go back to Zinc Binding Sites List in 6c7g
Zinc 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 Zinc with other atoms in the Zn 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:Zn1002

b:11.6
occ:1.00
 NE2 B:HIS696 2.0 6.4 1.0
OD2 B:ASP697 2.1 8.7 1.0
NE2 B:HIS660 2.2 8.4 1.0
OD1 B:ASP808 2.2 9.8 1.0
O B:HOH1118 2.3 8.2 1.0
O B:HOH1199 2.5 9.6 1.0
CE1 B:HIS696 3.0 6.2 1.0
CD2 B:HIS696 3.1 5.6 1.0
CD2 B:HIS660 3.1 6.9 1.0
CG B:ASP808 3.1 12.5 1.0
CG B:ASP697 3.2 6.0 1.0
CE1 B:HIS660 3.2 9.4 1.0
OD2 B:ASP808 3.3 12.5 1.0
OD1 B:ASP697 3.7 6.0 1.0
MG B:MG1003 4.0 6.4 1.0
O B:HOH1155 4.1 9.9 1.0
ND1 B:HIS696 4.1 8.7 1.0
CG B:HIS696 4.2 5.6 1.0
CD2 B:HIS656 4.2 11.9 1.0
O B:HOH1225 4.2 6.0 1.0
CG B:HIS660 4.3 7.5 1.0
ND1 B:HIS660 4.3 7.5 1.0
CB B:ASP697 4.3 8.0 1.0
NE2 B:HIS656 4.3 11.9 1.0
CB B:ASP808 4.5 8.9 1.0
O B:HOH1140 4.8 8.1 1.0
CG2 B:VAL664 4.8 6.2 1.0
CA B:ASP808 4.9 12.4 1.0
O B:ASP808 4.9 10.4 1.0

Zinc binding site 3 out of 4 in 6c7g

Go back to Zinc Binding Sites List in 6c7g
Zinc 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 Zinc with other atoms in the Zn 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:Zn1002

b:12.8
occ:1.00
 NE2 C:HIS660 2.0 8.8 1.0
NE2 C:HIS696 2.1 10.2 1.0
OD2 C:ASP697 2.1 12.8 1.0
OD1 C:ASP808 2.1 14.8 1.0
O C:HOH1161 2.2 13.2 1.0
O C:HOH1137 2.4 13.7 1.0
CD2 C:HIS660 3.0 10.3 1.0
CE1 C:HIS696 3.0 10.8 1.0
CD2 C:HIS696 3.0 16.2 1.0
CG C:ASP808 3.1 15.6 1.0
CE1 C:HIS660 3.1 9.6 1.0
CG C:ASP697 3.2 9.4 1.0
OD2 C:ASP808 3.3 16.2 1.0
OD1 C:ASP697 3.7 8.8 1.0
MG C:MG1003 4.0 9.2 1.0
O C:HOH1148 4.1 12.4 1.0
ND1 C:HIS696 4.1 11.6 1.0
CG C:HIS660 4.1 10.7 1.0
CG C:HIS696 4.2 11.2 1.0
ND1 C:HIS660 4.2 10.5 1.0
CD2 C:HIS656 4.2 9.2 1.0
O C:HOH1197 4.2 8.5 1.0
NE2 C:HIS656 4.3 10.1 1.0
CB C:ASP697 4.4 9.7 1.0
CB C:ASP808 4.5 13.4 1.0
O C:HOH1116 4.8 10.2 1.0
CG2 C:VAL664 4.9 10.7 1.0
CA C:ASP808 4.9 13.2 1.0
O C:ASP808 5.0 14.8 1.0

Zinc binding site 4 out of 4 in 6c7g

Go back to Zinc Binding Sites List in 6c7g
Zinc 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 Zinc with other atoms in the Zn 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:Zn1002

b:13.5
occ:1.00
 OD1 D:ASP808 2.0 14.8 1.0
OD2 D:ASP697 2.0 11.9 1.0
NE2 D:HIS660 2.0 11.1 1.0
NE2 D:HIS696 2.1 12.3 1.0
O D:HOH1193 2.2 8.2 1.0
O D:HOH1107 2.4 15.8 1.0
CG D:ASP808 2.9 14.5 1.0
CE1 D:HIS660 3.0 11.4 1.0
CD2 D:HIS696 3.0 13.8 1.0
CD2 D:HIS660 3.0 11.9 1.0
CG D:ASP697 3.1 10.9 1.0
CE1 D:HIS696 3.1 13.7 1.0
OD2 D:ASP808 3.2 14.9 1.0
OD1 D:ASP697 3.7 11.9 1.0
MG D:MG1003 4.0 8.6 1.0
O D:HOH1161 4.0 12.4 1.0
ND1 D:HIS660 4.1 12.4 1.0
CG D:HIS660 4.2 12.7 1.0
CG D:HIS696 4.2 11.4 1.0
ND1 D:HIS696 4.2 12.5 1.0
CD2 D:HIS656 4.2 10.3 1.0
O D:HOH1216 4.2 7.5 1.0
CB D:ASP697 4.3 11.3 1.0
CB D:ASP808 4.4 13.1 1.0
NE2 D:HIS656 4.5 13.6 1.0
O D:HOH1132 4.8 7.4 1.0
CA D:ASP808 4.9 13.5 1.0
CG2 D:VAL664 4.9 12.5 1.0
O D:ASP808 5.0 13.8 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 18:32:00 2024

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