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Zinc in PDB 5uoy: Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 16J (6-(4-Methoxybenzyl)-9-((Tetrahydro-2H-Pyran-4-Yl) Methyl)-8,9,10,11-Tetrahydropyrido[4',3':4,5]Thieno[3,2-E][1,2, 4]Triazolo[1,5-C]Pyrimidin-5(6H)-One)

Enzymatic activity of Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 16J (6-(4-Methoxybenzyl)-9-((Tetrahydro-2H-Pyran-4-Yl) Methyl)-8,9,10,11-Tetrahydropyrido[4',3':4,5]Thieno[3,2-E][1,2, 4]Triazolo[1,5-C]Pyrimidin-5(6H)-One)

All present enzymatic activity of Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 16J (6-(4-Methoxybenzyl)-9-((Tetrahydro-2H-Pyran-4-Yl) Methyl)-8,9,10,11-Tetrahydropyrido[4',3':4,5]Thieno[3,2-E][1,2, 4]Triazolo[1,5-C]Pyrimidin-5(6H)-One):
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 16J (6-(4-Methoxybenzyl)-9-((Tetrahydro-2H-Pyran-4-Yl) Methyl)-8,9,10,11-Tetrahydropyrido[4',3':4,5]Thieno[3,2-E][1,2, 4]Triazolo[1,5-C]Pyrimidin-5(6H)-One), PDB code: 5uoy was solved by E.P.Cedervall, C.K.Allerston, R.Xu, V.Sridhar, R.Barker, K.Aertgeerts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.88 / 1.82
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.507, 87.507, 134.714, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.1

Other elements in 5uoy:

The structure of Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 16J (6-(4-Methoxybenzyl)-9-((Tetrahydro-2H-Pyran-4-Yl) Methyl)-8,9,10,11-Tetrahydropyrido[4',3':4,5]Thieno[3,2-E][1,2, 4]Triazolo[1,5-C]Pyrimidin-5(6H)-One) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 16J (6-(4-Methoxybenzyl)-9-((Tetrahydro-2H-Pyran-4-Yl) Methyl)-8,9,10,11-Tetrahydropyrido[4',3':4,5]Thieno[3,2-E][1,2, 4]Triazolo[1,5-C]Pyrimidin-5(6H)-One) (pdb code 5uoy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 16J (6-(4-Methoxybenzyl)-9-((Tetrahydro-2H-Pyran-4-Yl) Methyl)-8,9,10,11-Tetrahydropyrido[4',3':4,5]Thieno[3,2-E][1,2, 4]Triazolo[1,5-C]Pyrimidin-5(6H)-One), PDB code: 5uoy:

Zinc binding site 1 out of 1 in 5uoy

Go back to Zinc Binding Sites List in 5uoy
Zinc binding site 1 out of 1 in the Crystal Structure of Human PDE1B Catalytic Domain in Complex with Inhibitor 16J (6-(4-Methoxybenzyl)-9-((Tetrahydro-2H-Pyran-4-Yl) Methyl)-8,9,10,11-Tetrahydropyrido[4',3':4,5]Thieno[3,2-E][1,2, 4]Triazolo[1,5-C]Pyrimidin-5(6H)-One)


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 PDE1B Catalytic Domain in Complex with Inhibitor 16J (6-(4-Methoxybenzyl)-9-((Tetrahydro-2H-Pyran-4-Yl) Methyl)-8,9,10,11-Tetrahydropyrido[4',3':4,5]Thieno[3,2-E][1,2, 4]Triazolo[1,5-C]Pyrimidin-5(6H)-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:29.6
occ:1.00
 OD2 A:ASP264 2.1 23.9 1.0
OD1 A:ASP370 2.1 22.5 1.0
NE2 A:HIS263 2.2 20.9 1.0
NE2 A:HIS227 2.3 21.6 1.0
O A:HOH712 2.3 22.9 1.0
O A:HOH755 2.5 26.9 1.0
CG A:ASP370 3.0 30.3 1.0
CD2 A:HIS263 3.1 23.5 1.0
CD2 A:HIS227 3.1 20.9 1.0
CG A:ASP264 3.1 21.8 1.0
CE1 A:HIS263 3.2 23.1 1.0
OD2 A:ASP370 3.3 33.6 1.0
CE1 A:HIS227 3.4 23.3 1.0
OD1 A:ASP264 3.6 22.2 1.0
MG A:MG602 3.7 23.6 1.0
O A:HOH753 3.9 30.6 1.0
O A:HOH803 4.0 21.4 1.0
CG A:HIS263 4.2 19.3 1.0
CD2 A:HIS223 4.2 20.8 1.0
ND1 A:HIS263 4.3 20.5 1.0
CG A:HIS227 4.3 22.2 1.0
NE2 A:HIS223 4.3 24.8 1.0
CB A:ASP264 4.3 20.0 1.0
CB A:ASP370 4.4 25.8 1.0
ND1 A:HIS227 4.4 22.8 1.0
O A:HOH740 4.7 21.8 1.0
O A:HOH824 4.8 54.8 1.0
CG2 A:VAL231 4.8 22.9 1.0
CA A:ASP370 4.8 25.6 1.0
O A:ASP370 4.9 23.9 1.0

Reference:

B.Dyck, B.Branstetter, T.Gharbaoui, A.R.Hudson, J.G.Breitenbucher, L.Gomez, I.Botrous, T.Marrone, R.Barido, C.K.Allerston, E.P.Cedervall, R.Xu, V.Sridhar, R.Barker, K.Aertgeerts, K.Schmelzer, D.Neul, D.Lee, M.E.Massari, C.B.Andersen, K.Sebring, X.Zhou, R.Petroski, J.Limberis, M.Augustin, L.E.Chun, T.E.Edwards, M.Peters, A.Tabatabaei. Discovery of Selective Phosphodiesterase 1 Inhibitors with Memory Enhancing Properties. J. Med. Chem. V. 60 3472 2017.
ISSN: ISSN 1520-4804
PubMed: 28406621
DOI: 10.1021/ACS.JMEDCHEM.7B00302
Page generated: Mon Oct 28 11:24:27 2024

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