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

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 2A in Complex with 1-[(3, 4-Difluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine, PDB code: 5tzw 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) 68.91 / 1.59
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.806, 72.997, 91.000, 109.22, 90.96, 91.07
R / Rfree (%) 18.8 / 22.5

Other elements in 5tzw:

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

Fluorine (F) 20 atoms
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-[(3, 4-Difluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine (pdb code 5tzw). 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-[(3, 4-Difluorophenyl)Carbonyl]-3,3-Difluoro-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine, PDB code: 5tzw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5tzw

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

b:14.8
occ:1.00
 O A:HOH1210 2.0 15.1 1.0
NE2 A:HIS660 2.1 12.4 1.0
NE2 A:HIS696 2.1 11.2 1.0
OD2 A:ASP697 2.1 13.0 1.0
OD1 A:ASP808 2.2 12.3 1.0
CD2 A:HIS696 3.0 12.8 1.0
O A:HOH1219 3.0 16.4 1.0
CD2 A:HIS660 3.0 13.7 1.0
CE1 A:HIS660 3.1 11.3 1.0
CG A:ASP808 3.1 10.3 1.0
CE1 A:HIS696 3.1 10.3 1.0
CG A:ASP697 3.1 10.1 1.0
OD2 A:ASP808 3.3 16.6 1.0
OD1 A:ASP697 3.6 12.1 1.0
MG A:MG1003 3.7 11.7 1.0
CG A:HIS696 4.1 9.6 1.0
CG A:HIS660 4.2 14.4 1.0
ND1 A:HIS660 4.2 13.1 1.0
ND1 A:HIS696 4.2 9.4 1.0
CD2 A:HIS656 4.2 16.4 1.0
O A:HOH1261 4.2 16.1 1.0
O A:HOH1196 4.3 13.8 1.0
CB A:ASP697 4.3 10.5 1.0
NE2 A:HIS656 4.5 17.2 1.0
CB A:ASP808 4.5 12.5 1.0
O A:HOH1152 4.5 15.0 1.0
CG2 A:VAL664 4.7 11.9 1.0
CA A:ASP808 4.9 14.3 1.0
O A:ASP808 5.0 13.9 1.0

Zinc binding site 2 out of 4 in 5tzw

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

b:15.1
occ:1.00
 O B:HOH1126 2.1 13.7 1.0
NE2 B:HIS696 2.1 8.9 1.0
OD2 B:ASP697 2.1 12.0 1.0
CE1 B:HIS660 2.1 11.7 1.0
OD1 B:ASP808 2.2 14.1 1.0
CD2 B:HIS696 2.9 13.5 1.0
NE2 B:HIS660 3.0 18.4 1.0
O B:HOH1263 3.1 22.4 1.0
CG B:ASP808 3.1 15.9 1.0
ND1 B:HIS660 3.1 20.2 1.0
CG B:ASP697 3.1 11.2 1.0
CE1 B:HIS696 3.1 13.0 1.0
OD2 B:ASP808 3.3 17.8 1.0
OD1 B:ASP697 3.6 11.4 1.0
MG B:MG1003 3.8 14.2 1.0
CG B:HIS696 4.1 10.3 1.0
O B:HOH1241 4.1 19.0 1.0
ND1 B:HIS696 4.2 11.1 1.0
CD2 B:HIS656 4.2 17.6 1.0
CD2 B:HIS660 4.2 9.1 1.0
CG B:HIS660 4.2 11.6 1.0
O B:HOH1207 4.3 13.2 1.0
CB B:ASP697 4.3 9.4 1.0
CB B:ASP808 4.5 11.9 1.0
NE2 B:HIS656 4.5 16.8 1.0
O B:HOH1153 4.5 13.1 1.0
CG2 B:VAL664 4.8 14.0 1.0
CA B:ASP808 4.9 13.3 1.0

Zinc binding site 3 out of 4 in 5tzw

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

b:16.7
occ:1.00
 OD2 C:ASP697 2.0 15.5 1.0
NE2 C:HIS696 2.1 13.7 1.0
O C:HOH1152 2.1 13.7 1.0
NE2 C:HIS660 2.1 14.7 1.0
OD1 C:ASP808 2.1 15.7 1.0
O C:HOH1151 2.9 22.3 1.0
CD2 C:HIS696 2.9 14.9 1.0
CD2 C:HIS660 3.0 13.7 1.0
CG C:ASP808 3.1 17.5 1.0
CG C:ASP697 3.1 14.7 1.0
CE1 C:HIS696 3.1 14.6 1.0
CE1 C:HIS660 3.2 15.7 1.0
OD2 C:ASP808 3.3 17.8 1.0
OD1 C:ASP697 3.6 13.7 1.0
MG C:MG1003 3.8 13.1 1.0
CD2 C:HIS656 4.1 15.4 1.0
CG C:HIS696 4.1 13.9 1.0
O C:HOH1200 4.2 18.6 1.0
ND1 C:HIS696 4.2 15.7 1.0
CG C:HIS660 4.2 13.0 1.0
ND1 C:HIS660 4.2 14.4 1.0
O C:HOH1228 4.3 13.1 1.0
CB C:ASP697 4.3 13.8 1.0
NE2 C:HIS656 4.4 17.4 1.0
CB C:ASP808 4.5 15.2 1.0
O C:HOH1143 4.6 14.6 1.0
CG2 C:VAL664 4.8 14.3 1.0
CA C:ASP808 4.9 14.2 1.0
O C:ASP808 5.0 15.9 1.0

Zinc binding site 4 out of 4 in 5tzw

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

b:16.7
occ:1.00
 O D:HOH1168 2.1 16.2 1.0
OD2 D:ASP697 2.1 13.5 1.0
NE2 D:HIS696 2.1 12.8 1.0
CE1 D:HIS660 2.2 11.9 1.0
OD1 D:ASP808 2.2 13.8 1.0
O D:HOH1237 2.9 19.4 1.0
CD2 D:HIS696 2.9 11.8 1.0
NE2 D:HIS660 3.1 18.5 1.0
CG D:ASP808 3.1 12.7 1.0
CG D:ASP697 3.1 12.6 1.0
ND1 D:HIS660 3.2 19.8 1.0
CE1 D:HIS696 3.2 12.7 1.0
OD2 D:ASP808 3.3 16.6 1.0
OD1 D:ASP697 3.6 11.4 1.0
MG D:MG1003 3.7 12.5 1.0
CG D:HIS696 4.1 13.8 1.0
O D:HOH1210 4.2 18.1 1.0
CD2 D:HIS656 4.2 14.5 1.0
ND1 D:HIS696 4.2 14.0 1.0
O D:HOH1249 4.2 13.6 1.0
CD2 D:HIS660 4.3 13.0 1.0
CB D:ASP697 4.3 14.3 1.0
CG D:HIS660 4.3 17.3 1.0
NE2 D:HIS656 4.4 14.0 1.0
O D:HOH1148 4.5 13.3 1.0
CB D:ASP808 4.5 11.4 1.0
CG2 D:VAL664 4.9 16.3 1.0
CA D:ASP808 4.9 13.4 1.0
O D:ASP808 5.0 16.8 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 09:01:26 2024

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