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Magnesium 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
Zinc (Zn) 4 atoms
Iodine (I) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 5u00

Go back to Magnesium Binding Sites List in 5u00
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1003

b:9.3
occ:1.00
 O A:HOH1195 2.0 12.7 1.0
OD1 A:ASP697 2.1 8.2 1.0
O A:HOH1136 2.1 9.9 1.0
O A:HOH1228 2.1 12.6 1.0
O A:HOH1211 2.1 10.0 1.0
O A:HOH1173 2.2 11.2 1.0
CG A:ASP697 3.0 9.5 1.0
OD2 A:ASP697 3.3 10.1 1.0
ZN A:ZN1002 3.7 12.4 1.0
O A:HOH1230 3.9 16.6 1.0
O A:HOH1342 4.0 20.5 1.0
OE2 A:GLU727 4.1 18.6 1.0
NE2 A:HIS730 4.2 10.4 1.0
CD2 A:HIS696 4.2 9.1 1.0
OG1 A:THR768 4.2 12.2 1.0
O A:HOH1252 4.2 13.1 1.0
O A:HIS696 4.3 9.4 1.0
CD2 A:HIS730 4.4 9.8 1.0
NE2 A:HIS656 4.4 13.8 1.0
CB A:ASP697 4.4 10.3 1.0
OD2 A:ASP808 4.5 14.9 1.0
CD2 A:HIS656 4.5 13.7 1.0
CB A:THR768 4.5 11.6 1.0
NE2 A:HIS696 4.5 10.1 1.0
CD2 A:HIS700 4.6 11.7 1.0
O A:THR768 4.7 13.6 1.0
CA A:ASP697 4.8 9.4 1.0
NE2 A:HIS700 4.8 13.5 1.0
O A:HOH1108 4.8 19.9 1.0
CG A:GLU727 4.9 13.7 1.0
CD A:GLU727 4.9 15.3 1.0

Magnesium binding site 2 out of 4 in 5u00

Go back to Magnesium Binding Sites List in 5u00
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1003

b:10.8
occ:1.00
 O B:HOH1234 2.1 12.6 1.0
OD1 B:ASP697 2.1 9.4 1.0
O B:HOH1155 2.1 11.0 1.0
O B:HOH1130 2.2 13.4 1.0
O B:HOH1162 2.2 11.4 1.0
O B:HOH1174 2.2 10.4 1.0
CG B:ASP697 3.1 8.9 1.0
OD2 B:ASP697 3.4 10.7 1.0
ZN B:ZN1002 3.7 13.0 1.0
O B:HOH1305 3.9 19.6 1.0
O B:HOH1251 4.0 16.9 1.0
NE2 B:HIS730 4.1 9.2 1.0
OE2 B:GLU727 4.1 15.9 1.0
OG1 B:THR768 4.2 12.0 1.0
CD2 B:HIS696 4.2 8.9 1.0
O B:HOH1270 4.2 16.0 1.0
O B:HIS696 4.3 9.1 1.0
CD2 B:HIS730 4.3 11.4 1.0
CB B:ASP697 4.4 7.7 1.0
NE2 B:HIS656 4.5 16.1 1.0
CD2 B:HIS656 4.5 13.2 1.0
CD2 B:HIS700 4.5 12.1 1.0
OD2 B:ASP808 4.5 14.7 1.0
NE2 B:HIS696 4.5 7.9 1.0
CB B:THR768 4.6 10.5 1.0
NE2 B:HIS700 4.8 14.2 1.0
O B:THR768 4.8 13.2 1.0
CA B:ASP697 4.8 8.4 1.0
O B:HOH1180 4.9 20.0 1.0
CD B:GLU727 5.0 14.7 1.0
CG B:GLU727 5.0 12.2 1.0

Magnesium binding site 3 out of 4 in 5u00

Go back to Magnesium Binding Sites List in 5u00
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1003

b:12.6
occ:1.00
 O C:HOH1130 2.1 12.1 1.0
O C:HOH1237 2.1 11.6 1.0
OD1 C:ASP697 2.1 11.9 1.0
O C:HOH1132 2.1 12.7 1.0
O C:HOH1178 2.1 11.3 1.0
O C:HOH1200 2.2 11.7 1.0
CG C:ASP697 3.1 11.4 1.0
OD2 C:ASP697 3.4 11.7 1.0
ZN C:ZN1002 3.8 13.9 1.0
O C:HOH1303 3.9 22.8 1.0
OE2 C:GLU727 4.1 17.0 1.0
O C:HOH1219 4.1 19.4 1.0
NE2 C:HIS730 4.2 11.6 1.0
OG1 C:THR768 4.2 13.7 1.0
CD2 C:HIS696 4.2 12.5 1.0
O C:HOH1225 4.2 14.2 1.0
O C:HIS696 4.3 10.4 1.0
CD2 C:HIS700 4.4 12.9 1.0
CD2 C:HIS730 4.4 13.9 1.0
CD2 C:HIS656 4.5 18.0 1.0
OD2 C:ASP808 4.5 16.2 1.0
CB C:ASP697 4.5 13.9 1.0
NE2 C:HIS656 4.5 18.1 1.0
NE2 C:HIS696 4.6 12.1 1.0
CB C:THR768 4.6 12.7 1.0
O C:THR768 4.7 14.8 1.0
NE2 C:HIS700 4.7 14.1 1.0
O C:HOH1128 4.8 19.8 1.0
CA C:ASP697 4.8 11.1 1.0
CG C:GLU727 4.9 10.9 1.0
CD C:GLU727 4.9 15.2 1.0

Magnesium binding site 4 out of 4 in 5u00

Go back to Magnesium Binding Sites List in 5u00
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1003

b:11.4
occ:1.00
 OD1 D:ASP697 2.0 10.6 1.0
O D:HOH1240 2.0 12.3 1.0
O D:HOH1131 2.0 12.6 1.0
O D:HOH1147 2.1 11.3 1.0
O D:HOH1175 2.1 11.7 1.0
O D:HOH1208 2.2 12.3 1.0
CG D:ASP697 3.0 10.9 1.0
OD2 D:ASP697 3.4 13.9 1.0
ZN D:ZN1002 3.7 13.5 1.0
O D:HOH1302 3.9 22.6 1.0
O D:HOH1209 3.9 16.6 1.0
OE2 D:GLU727 4.1 13.7 1.0
CD2 D:HIS696 4.2 13.0 1.0
NE2 D:HIS730 4.2 10.2 1.0
O D:HOH1200 4.2 16.3 1.0
OG1 D:THR768 4.2 11.6 1.0
O D:HIS696 4.4 11.6 1.0
OD2 D:ASP808 4.4 18.9 1.0
CB D:ASP697 4.4 11.4 1.0
CD2 D:HIS700 4.5 14.3 1.0
NE2 D:HIS656 4.5 15.3 1.0
CD2 D:HIS730 4.5 10.8 1.0
CD2 D:HIS656 4.5 16.4 1.0
CB D:THR768 4.5 11.2 1.0
NE2 D:HIS696 4.6 11.4 1.0
O D:THR768 4.6 14.2 1.0
NE2 D:HIS700 4.7 13.7 1.0
CA D:ASP697 4.8 11.4 1.0
CG D:GLU727 5.0 11.3 1.0
CD D:GLU727 5.0 12.7 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 Sep 30 05:07:20 2024

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