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Zinc in PDB 5tza: Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine, PDB code: 5tza 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) 55.77 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.799, 73.444, 91.614, 109.36, 91.17, 91.14
R / Rfree (%) 16.5 / 19.7

Other elements in 5tza:

The structure of Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine (pdb code 5tza). 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 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine, PDB code: 5tza:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5tza

Go back to Zinc Binding Sites List in 5tza
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine


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 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:11.8
occ:1.00
 NE2 A:HIS696 2.1 7.6 1.0
OD2 A:ASP697 2.1 9.2 1.0
O A:HOH1174 2.1 10.0 1.0
NE2 A:HIS660 2.1 9.9 1.0
OD1 A:ASP808 2.2 11.2 1.0
CD2 A:HIS696 2.9 11.1 1.0
O A:HOH1277 3.0 14.8 1.0
CD2 A:HIS660 3.1 10.5 1.0
CG A:ASP697 3.1 7.7 1.0
CG A:ASP808 3.1 8.9 1.0
CE1 A:HIS696 3.1 7.5 1.0
CE1 A:HIS660 3.2 9.5 1.0
OD2 A:ASP808 3.4 13.6 1.0
OD1 A:ASP697 3.6 7.8 1.0
MG A:MG1003 3.7 8.7 1.0
CG A:HIS696 4.1 8.9 1.0
ND1 A:HIS696 4.2 7.5 1.0
CD2 A:HIS656 4.2 11.1 1.0
O A:HOH1242 4.2 14.7 1.0
CG A:HIS660 4.2 9.7 1.0
ND1 A:HIS660 4.2 8.5 1.0
CB A:ASP697 4.3 10.2 1.0
O A:HOH1234 4.3 10.2 1.0
CB A:ASP808 4.5 8.2 1.0
O A:HOH1154 4.5 8.3 1.0
NE2 A:HIS656 4.6 12.9 1.0
CG2 A:VAL664 4.8 9.9 1.0
CA A:ASP808 4.9 7.9 1.0
O A:ASP808 5.0 10.7 1.0

Zinc binding site 2 out of 4 in 5tza

Go back to Zinc Binding Sites List in 5tza
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine


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 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:12.7
occ:1.00
 O B:HOH1130 2.0 10.8 1.0
NE2 B:HIS696 2.1 9.4 1.0
OD2 B:ASP697 2.1 10.3 1.0
NE2 B:HIS660 2.1 11.7 1.0
OD1 B:ASP808 2.2 12.9 1.0
CD2 B:HIS696 3.0 9.5 1.0
CD2 B:HIS660 3.0 11.6 1.0
O B:HOH1235 3.0 17.6 1.0
CG B:ASP808 3.1 11.8 1.0
CG B:ASP697 3.1 10.0 1.0
CE1 B:HIS696 3.1 10.8 1.0
CE1 B:HIS660 3.2 12.2 1.0
OD2 B:ASP808 3.3 13.3 1.0
OD1 B:ASP697 3.6 9.7 1.0
MG B:MG1003 3.7 10.2 1.0
O B:HOH1240 4.1 14.4 1.0
CG B:HIS696 4.1 11.4 1.0
CG B:HIS660 4.2 11.5 1.0
ND1 B:HIS696 4.2 10.2 1.0
CD2 B:HIS656 4.2 14.5 1.0
ND1 B:HIS660 4.2 11.6 1.0
O B:HOH1249 4.2 10.7 1.0
CB B:ASP697 4.3 10.9 1.0
CB B:ASP808 4.5 9.1 1.0
O B:HOH1156 4.5 9.8 1.0
NE2 B:HIS656 4.5 14.7 1.0
CG2 B:VAL664 4.8 9.8 1.0
CA B:ASP808 4.9 9.9 1.0
O B:ASP808 5.0 13.4 1.0

Zinc binding site 3 out of 4 in 5tza

Go back to Zinc Binding Sites List in 5tza
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine


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 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:13.3
occ:1.00
 O C:HOH1132 2.0 12.3 1.0
OD2 C:ASP697 2.1 11.2 1.0
NE2 C:HIS660 2.1 10.3 1.0
NE2 C:HIS696 2.1 10.2 1.0
OD1 C:ASP808 2.2 11.3 1.0
CD2 C:HIS696 3.0 13.1 1.0
O C:HOH1231 3.0 19.2 1.0
CD2 C:HIS660 3.0 10.7 1.0
CG C:ASP808 3.1 12.0 1.0
CG C:ASP697 3.1 13.1 1.0
CE1 C:HIS660 3.1 13.1 1.0
CE1 C:HIS696 3.2 11.1 1.0
OD2 C:ASP808 3.3 15.5 1.0
OD1 C:ASP697 3.6 10.1 1.0
MG C:MG1003 3.7 11.1 1.0
CD2 C:HIS656 4.1 14.2 1.0
CG C:HIS696 4.2 12.4 1.0
CG C:HIS660 4.2 11.5 1.0
O C:HOH1237 4.2 15.2 1.0
ND1 C:HIS660 4.2 11.3 1.0
ND1 C:HIS696 4.2 12.0 1.0
O C:HOH1229 4.3 11.0 1.0
CB C:ASP697 4.3 12.9 1.0
CB C:ASP808 4.5 10.6 1.0
NE2 C:HIS656 4.5 18.0 1.0
O C:HOH1121 4.6 11.5 1.0
CG2 C:VAL664 4.8 11.7 1.0
CA C:ASP808 4.9 13.5 1.0

Zinc binding site 4 out of 4 in 5tza

Go back to Zinc Binding Sites List in 5tza
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A with 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine


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 3-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl-1-[(Naphthalene-2-Yl) Carbonyl]Piperidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:13.0
occ:1.00
 NE2 D:HIS696 2.0 10.0 1.0
OD2 D:ASP697 2.1 10.1 1.0
O D:HOH1167 2.1 11.7 1.0
NE2 D:HIS660 2.1 10.6 1.0
OD1 D:ASP808 2.2 13.7 1.0
CD2 D:HIS696 3.0 11.6 1.0
CD2 D:HIS660 3.0 11.3 1.0
O D:HOH1252 3.0 16.0 1.0
CG D:ASP808 3.1 12.3 1.0
CE1 D:HIS696 3.1 13.7 1.0
CG D:ASP697 3.1 9.4 1.0
CE1 D:HIS660 3.2 14.7 1.0
OD2 D:ASP808 3.3 14.3 1.0
OD1 D:ASP697 3.6 9.1 1.0
MG D:MG1003 3.7 9.5 1.0
CD2 D:HIS656 4.1 12.3 1.0
CG D:HIS696 4.1 9.2 1.0
O D:HOH1178 4.1 15.1 1.0
ND1 D:HIS696 4.1 13.1 1.0
CG D:HIS660 4.2 11.4 1.0
ND1 D:HIS660 4.2 11.2 1.0
O D:HOH1278 4.3 10.7 1.0
CB D:ASP697 4.3 11.5 1.0
NE2 D:HIS656 4.4 13.3 1.0
O D:HOH1143 4.5 9.3 1.0
CB D:ASP808 4.5 9.9 1.0
CG2 D:VAL664 4.8 10.4 1.0
CA D:ASP808 4.9 10.9 1.0
O D:ASP808 5.0 12.9 1.0

Reference:

L.Gomez, M.E.Massari, T.Vickers, G.Freestone, W.Vernier, K.Ly, R.Xu, M.Mccarrick, T.Marrone, M.Metz, Y.G.Yan, Z.W.Yoder, R.Lemus, N.J.Broadbent, R.Barido, N.Warren, K.Schmelzer, D.Neul, D.Lee, C.B.Andersen, K.Sebring, K.Aertgeerts, X.Zhou, A.Tabatabaei, M.Peters, J.G.Breitenbucher. Design and Synthesis of Novel and Selective Phosphodiesterase 2 (PDE2A) Inhibitors For the Treatment of Memory Disorders. J. Med. Chem. V. 60 2037 2017.
ISSN: ISSN 1520-4804
PubMed: 28165743
DOI: 10.1021/ACS.JMEDCHEM.6B01793
Page generated: Mon Oct 28 08:59:46 2024

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