Atomistry » Zinc » PDB 5tt5-5u0c » 5u00
Atomistry »
  Zinc »
    PDB 5tt5-5u0c »
      5u00 »

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

Go back to Zinc Binding Sites List in 5u00
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

Go back to Zinc Binding Sites List in 5u00
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy