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Zinc in PDB 5u00: Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine, PDB code: 5u00 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) 65.53 / 1.41
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.986, 73.249, 91.206, 109.38, 90.79, 91.10
R / Rfree (%) 19.9 / 22.8

Other elements in 5u00:

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

Fluorine (F) 12 atoms
Magnesium (Mg) 4 atoms
Iodine (I) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine (pdb code 5u00). 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 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-5-{5-Methyl-[1,2, 4]Triazolo[1,5-A]Pyrimidin-7-Yl}Piperidine, PDB code: 5u00:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5u00

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:12.4
occ:1.00
 O A:HOH1195 2.0 12.7 1.0
NE2 A:HIS696 2.1 10.1 1.0
OD2 A:ASP697 2.1 10.1 1.0
NE2 A:HIS660 2.1 11.2 1.0
OD1 A:ASP808 2.2 11.1 1.0
O A:HOH1230 2.6 16.6 1.0
CD2 A:HIS696 3.0 9.1 1.0
CD2 A:HIS660 3.0 13.0 1.0
CG A:ASP808 3.1 9.6 1.0
CE1 A:HIS696 3.1 11.5 1.0
CG A:ASP697 3.2 9.5 1.0
CE1 A:HIS660 3.2 9.5 1.0
OD2 A:ASP808 3.3 14.9 1.0
OD1 A:ASP697 3.6 8.2 1.0
MG A:MG1003 3.7 9.3 1.0
CG A:HIS696 4.2 8.9 1.0
CD2 A:HIS656 4.2 13.7 1.0
ND1 A:HIS696 4.2 9.2 1.0
CG A:HIS660 4.2 9.5 1.0
O A:HOH1219 4.2 16.5 1.0
ND1 A:HIS660 4.2 12.4 1.0
O A:HOH1228 4.3 12.6 1.0
CB A:ASP697 4.4 10.3 1.0
NE2 A:HIS656 4.4 13.8 1.0
CB A:ASP808 4.5 10.3 1.0
O A:HOH1136 4.5 9.9 1.0
CG2 A:VAL664 4.8 9.2 1.0
CA A:ASP808 4.9 10.9 1.0
O A:ASP808 5.0 11.8 1.0

Zinc binding site 2 out of 4 in 5u00

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:13.0
occ:1.00
 O B:HOH1130 2.1 13.4 1.0
NE2 B:HIS696 2.1 7.9 1.0
OD2 B:ASP697 2.1 10.7 1.0
NE2 B:HIS660 2.1 11.9 1.0
OD1 B:ASP808 2.1 11.2 1.0
O B:HOH1251 3.0 16.9 1.0
CD2 B:HIS696 3.0 8.9 1.0
CD2 B:HIS660 3.1 12.0 1.0
CG B:ASP808 3.1 11.7 1.0
CE1 B:HIS696 3.1 14.9 1.0
CG B:ASP697 3.1 8.9 1.0
CE1 B:HIS660 3.2 10.6 1.0
OD2 B:ASP808 3.4 14.7 1.0
OD1 B:ASP697 3.6 9.4 1.0
MG B:MG1003 3.7 10.8 1.0
CG B:HIS696 4.2 11.9 1.0
O B:HOH1234 4.2 12.6 1.0
CD2 B:HIS656 4.2 13.2 1.0
ND1 B:HIS696 4.2 11.4 1.0
O B:HOH1222 4.2 17.8 1.0
CG B:HIS660 4.2 10.5 1.0
ND1 B:HIS660 4.2 10.1 1.0
CB B:ASP697 4.4 7.7 1.0
NE2 B:HIS656 4.5 16.1 1.0
CB B:ASP808 4.5 10.9 1.0
O B:HOH1155 4.5 11.0 1.0
CG2 B:VAL664 4.8 9.5 1.0
CA B:ASP808 4.9 11.8 1.0

Zinc binding site 3 out of 4 in 5u00

Go back to Zinc Binding Sites List in 5u00
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:13.9
occ:1.00
 O C:HOH1132 2.0 12.7 1.0
NE2 C:HIS696 2.1 12.1 1.0
OD1 C:ASP808 2.1 14.1 1.0
OD2 C:ASP697 2.1 11.7 1.0
NE2 C:HIS660 2.1 11.2 1.0
CD2 C:HIS696 3.0 12.5 1.0
CG C:ASP808 3.0 15.6 1.0
O C:HOH1219 3.0 19.4 1.0
CD2 C:HIS660 3.1 11.6 1.0
CE1 C:HIS696 3.1 14.1 1.0
CE1 C:HIS660 3.1 11.8 1.0
CG C:ASP697 3.2 11.4 1.0
OD2 C:ASP808 3.2 16.2 1.0
OD1 C:ASP697 3.6 11.9 1.0
MG C:MG1003 3.8 12.6 1.0
CG C:HIS696 4.1 12.6 1.0
CD2 C:HIS656 4.2 18.0 1.0
ND1 C:HIS696 4.2 14.4 1.0
CG C:HIS660 4.2 12.6 1.0
O C:HOH1170 4.2 17.1 1.0
ND1 C:HIS660 4.2 13.1 1.0
O C:HOH1237 4.3 11.6 1.0
CB C:ASP697 4.4 13.9 1.0
CB C:ASP808 4.5 11.9 1.0
NE2 C:HIS656 4.5 18.1 1.0
O C:HOH1130 4.6 12.1 1.0
CG2 C:VAL664 4.9 13.6 1.0
CA C:ASP808 4.9 12.7 1.0

Zinc binding site 4 out of 4 in 5u00

Go back to Zinc Binding Sites List in 5u00
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 2A in Complex with 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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 3,3- Difluoro-1-[(4-Fluoro-3-Iodophenyl)Carbonyl]-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:13.5
occ:1.00
 O D:HOH1131 2.0 12.6 1.0
NE2 D:HIS660 2.1 10.9 1.0
OD2 D:ASP697 2.1 13.9 1.0
NE2 D:HIS696 2.1 11.4 1.0
OD1 D:ASP808 2.2 13.9 1.0
O D:HOH1209 2.6 16.6 1.0
CD2 D:HIS696 3.0 13.0 1.0
CG D:ASP808 3.0 13.7 1.0
CD2 D:HIS660 3.1 12.5 1.0
CE1 D:HIS660 3.1 10.8 1.0
CG D:ASP697 3.1 10.9 1.0
OD2 D:ASP808 3.2 18.9 1.0
CE1 D:HIS696 3.2 16.2 1.0
OD1 D:ASP697 3.6 10.6 1.0
MG D:MG1003 3.7 11.4 1.0
CD2 D:HIS656 4.2 16.4 1.0
ND1 D:HIS660 4.2 16.1 1.0
CG D:HIS696 4.2 9.3 1.0
CG D:HIS660 4.2 11.9 1.0
O D:HOH1182 4.2 17.0 1.0
O D:HOH1240 4.2 12.3 1.0
ND1 D:HIS696 4.3 12.4 1.0
CB D:ASP697 4.3 11.4 1.0
NE2 D:HIS656 4.4 15.3 1.0
CB D:ASP808 4.5 11.7 1.0
O D:HOH1147 4.5 11.3 1.0
CG2 D:VAL664 4.9 11.3 1.0
CA D:ASP808 4.9 12.4 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 09:02:06 2024

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