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Zinc in PDB 5tz3: Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide, PDB code: 5tz3 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) 68.65 / 1.72
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.754, 72.727, 90.517, 109.21, 90.70, 91.19
R / Rfree (%) 19.1 / 23.3

Other elements in 5tz3:

The structure of Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide 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 in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide (pdb code 5tz3). 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 in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide, PDB code: 5tz3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5tz3

Go back to Zinc Binding Sites List in 5tz3
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- 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 in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:16.2
occ:1.00
 O A:HOH1139 2.0 12.6 1.0
OD2 A:ASP697 2.1 15.4 1.0
NE2 A:HIS696 2.1 17.5 1.0
NE2 A:HIS660 2.2 17.6 1.0
OD1 A:ASP808 2.2 14.3 1.0
CD2 A:HIS696 2.9 18.9 1.0
O A:HOH1203 3.1 20.8 1.0
CG A:ASP808 3.1 15.2 1.0
CE1 A:HIS660 3.1 14.3 1.0
CG A:ASP697 3.1 15.2 1.0
CD2 A:HIS660 3.2 14.2 1.0
CE1 A:HIS696 3.2 13.2 1.0
OD2 A:ASP808 3.3 21.2 1.0
OD1 A:ASP697 3.7 11.4 1.0
MG A:MG1003 3.7 12.7 1.0
O A:HOH1166 4.1 19.3 1.0
CG A:HIS696 4.1 9.5 1.0
CD2 A:HIS656 4.2 15.6 1.0
ND1 A:HIS696 4.2 12.4 1.0
ND1 A:HIS660 4.2 18.6 1.0
CG A:HIS660 4.3 17.8 1.0
CB A:ASP697 4.3 20.2 1.0
O A:HOH1221 4.3 13.5 1.0
CB A:ASP808 4.5 18.4 1.0
O A:HOH1135 4.5 11.6 1.0
NE2 A:HIS656 4.5 17.7 1.0
O A:HOH1285 4.7 26.2 1.0
CG2 A:VAL664 4.8 11.2 1.0
O A:ASP808 4.9 16.6 1.0
CA A:ASP808 4.9 12.8 1.0

Zinc binding site 2 out of 4 in 5tz3

Go back to Zinc Binding Sites List in 5tz3
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- 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 in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:17.0
occ:1.00
 O B:HOH1121 2.0 12.3 1.0
OD2 B:ASP697 2.1 12.1 1.0
NE2 B:HIS696 2.1 10.6 1.0
NE2 B:HIS660 2.2 19.0 1.0
OD1 B:ASP808 2.2 13.6 1.0
O B:HOH1190 2.8 25.5 1.0
CD2 B:HIS696 2.9 12.3 1.0
CD2 B:HIS660 3.0 11.1 1.0
CG B:ASP697 3.1 10.6 1.0
CG B:ASP808 3.1 19.9 1.0
CE1 B:HIS696 3.3 17.6 1.0
CE1 B:HIS660 3.3 12.2 1.0
OD2 B:ASP808 3.3 21.6 1.0
OD1 B:ASP697 3.6 9.9 1.0
MG B:MG1003 3.7 12.1 1.0
O B:HOH1170 4.1 18.1 1.0
CG B:HIS696 4.1 10.3 1.0
CD2 B:HIS656 4.1 14.3 1.0
O B:HOH1220 4.2 15.5 1.0
CG B:HIS660 4.2 12.4 1.0
ND1 B:HIS696 4.3 14.8 1.0
CB B:ASP697 4.3 17.0 1.0
ND1 B:HIS660 4.3 12.5 1.0
O B:HOH1129 4.4 14.3 1.0
NE2 B:HIS656 4.5 15.1 1.0
CB B:ASP808 4.5 15.6 1.0
CG2 B:VAL664 4.9 14.7 1.0
O B:ASP808 4.9 14.9 1.0
CA B:ASP808 4.9 13.1 1.0
O B:HOH1175 5.0 13.4 1.0

Zinc binding site 3 out of 4 in 5tz3

Go back to Zinc Binding Sites List in 5tz3
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- 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 in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:17.9
occ:1.00
 O C:HOH1114 2.0 14.5 1.0
OD2 C:ASP697 2.0 14.8 1.0
NE2 C:HIS660 2.1 17.2 1.0
OD1 C:ASP808 2.1 13.4 1.0
NE2 C:HIS696 2.1 12.2 1.0
CD2 C:HIS660 3.0 13.9 1.0
CD2 C:HIS696 3.0 14.4 1.0
CG C:ASP808 3.0 17.3 1.0
O C:HOH1139 3.1 27.0 1.0
CG C:ASP697 3.1 10.8 1.0
CE1 C:HIS660 3.2 18.5 1.0
CE1 C:HIS696 3.2 17.7 1.0
OD2 C:ASP808 3.3 23.1 1.0
OD1 C:ASP697 3.6 15.2 1.0
MG C:MG1003 3.7 14.6 1.0
CD2 C:HIS656 4.1 18.1 1.0
CG C:HIS696 4.2 15.3 1.0
CG C:HIS660 4.2 17.2 1.0
O C:HOH1150 4.2 15.6 1.0
ND1 C:HIS660 4.2 14.5 1.0
ND1 C:HIS696 4.2 16.3 1.0
CB C:ASP697 4.3 14.3 1.0
O C:HOH1211 4.3 14.9 1.0
CB C:ASP808 4.4 16.5 1.0
NE2 C:HIS656 4.5 20.8 1.0
O C:HOH1121 4.5 14.3 1.0
CA C:ASP808 4.9 18.1 1.0
CG2 C:VAL664 4.9 13.1 1.0
O C:HOH1240 4.9 30.2 1.0
O C:ASP808 4.9 19.4 1.0

Zinc binding site 4 out of 4 in 5tz3

Go back to Zinc Binding Sites List in 5tz3
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- 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 in Complex with [1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}-N-(Naphthalene-2-Yl)Piperidine-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1002

b:18.1
occ:1.00
 O D:HOH1168 2.1 15.8 1.0
NE2 D:HIS696 2.1 13.3 1.0
OD2 D:ASP697 2.1 17.2 1.0
NE2 D:HIS660 2.2 17.2 1.0
OD1 D:ASP808 2.2 19.7 1.0
O D:HOH1122 2.4 18.5 1.0
CD2 D:HIS696 3.0 14.4 1.0
CD2 D:HIS660 3.0 14.4 1.0
CG D:ASP808 3.1 18.9 1.0
CE1 D:HIS696 3.1 16.2 1.0
CG D:ASP697 3.2 12.6 1.0
CE1 D:HIS660 3.2 18.2 1.0
OD2 D:ASP808 3.3 19.7 1.0
MG D:MG1003 3.6 14.2 1.0
OD1 D:ASP697 3.6 11.9 1.0
CG D:HIS696 4.1 14.4 1.0
CD2 D:HIS656 4.2 14.3 1.0
ND1 D:HIS696 4.2 16.7 1.0
CG D:HIS660 4.2 15.3 1.0
O D:HOH1213 4.2 14.3 1.0
O D:HOH1182 4.2 20.1 1.0
ND1 D:HIS660 4.3 16.3 1.0
CB D:ASP697 4.3 13.1 1.0
NE2 D:HIS656 4.4 13.2 1.0
CB D:ASP808 4.5 13.7 1.0
O D:HOH1151 4.5 13.2 1.0
CG2 D:VAL664 4.8 15.0 1.0
O D:ASP808 4.9 20.5 1.0
CA D:ASP808 4.9 14.9 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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