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Zinc in PDB 4npw: Crystal Structure of Human PDE1B Bound to Inhibitor 19A (7,8- Dimethoxy-N-[(2S)-1-(3-Methyl-1H-Pyrazol-5-Yl)Propan-2-Yl]Quinazolin- 4-Amine)

Enzymatic activity of Crystal Structure of Human PDE1B Bound to Inhibitor 19A (7,8- Dimethoxy-N-[(2S)-1-(3-Methyl-1H-Pyrazol-5-Yl)Propan-2-Yl]Quinazolin- 4-Amine)

All present enzymatic activity of Crystal Structure of Human PDE1B Bound to Inhibitor 19A (7,8- Dimethoxy-N-[(2S)-1-(3-Methyl-1H-Pyrazol-5-Yl)Propan-2-Yl]Quinazolin- 4-Amine):
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human PDE1B Bound to Inhibitor 19A (7,8- Dimethoxy-N-[(2S)-1-(3-Methyl-1H-Pyrazol-5-Yl)Propan-2-Yl]Quinazolin- 4-Amine), PDB code: 4npw was solved by J.Pandit, A.Evdomikov, M.Mansour, S.Simons, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.82 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.782, 88.782, 134.806, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 20.9

Other elements in 4npw:

The structure of Crystal Structure of Human PDE1B Bound to Inhibitor 19A (7,8- Dimethoxy-N-[(2S)-1-(3-Methyl-1H-Pyrazol-5-Yl)Propan-2-Yl]Quinazolin- 4-Amine) 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 Bound to Inhibitor 19A (7,8- Dimethoxy-N-[(2S)-1-(3-Methyl-1H-Pyrazol-5-Yl)Propan-2-Yl]Quinazolin- 4-Amine) (pdb code 4npw). 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 Bound to Inhibitor 19A (7,8- Dimethoxy-N-[(2S)-1-(3-Methyl-1H-Pyrazol-5-Yl)Propan-2-Yl]Quinazolin- 4-Amine), PDB code: 4npw:

Zinc binding site 1 out of 1 in 4npw

Go back to Zinc Binding Sites List in 4npw
Zinc binding site 1 out of 1 in the Crystal Structure of Human PDE1B Bound to Inhibitor 19A (7,8- Dimethoxy-N-[(2S)-1-(3-Methyl-1H-Pyrazol-5-Yl)Propan-2-Yl]Quinazolin- 4-Amine)


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 Bound to Inhibitor 19A (7,8- Dimethoxy-N-[(2S)-1-(3-Methyl-1H-Pyrazol-5-Yl)Propan-2-Yl]Quinazolin- 4-Amine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:24.1
occ:1.00
 OD2 A:ASP264 2.0 19.1 1.0
OD1 A:ASP370 2.0 20.2 1.0
NE2 A:HIS227 2.1 18.6 1.0
NE2 A:HIS263 2.2 18.2 1.0
O A:HOH1116 2.3 22.2 1.0
O A:HOH1112 2.4 18.3 1.0
CD2 A:HIS263 3.0 18.7 1.0
CD2 A:HIS227 3.0 19.6 1.0
CG A:ASP370 3.0 22.6 1.0
CG A:ASP264 3.1 20.7 1.0
CE1 A:HIS227 3.2 18.6 1.0
CE1 A:HIS263 3.3 17.9 1.0
OD2 A:ASP370 3.4 26.0 1.0
OD1 A:ASP264 3.6 17.9 1.0
MG A:MG1002 3.9 19.2 1.0
O A:HOH1104 4.0 19.4 1.0
O A:HOH1115 4.1 18.9 1.0
NE2 A:HIS223 4.2 22.7 1.0
CD2 A:HIS223 4.2 22.5 1.0
CG A:HIS263 4.2 18.2 1.0
CG A:HIS227 4.2 17.9 1.0
CB A:ASP264 4.3 16.6 1.0
ND1 A:HIS227 4.3 18.9 1.0
ND1 A:HIS263 4.3 18.9 1.0
CB A:ASP370 4.3 17.6 1.0
CG2 A:VAL231 4.7 16.1 1.0
CA A:ASP370 4.8 16.6 1.0
O A:HOH1111 4.8 18.4 1.0
O A:ASP370 4.9 20.8 1.0

Reference:

J.M.Humphrey, E.X.Yang, C.W.Am Ende, E.P.Arnold, J.L.Head, S.Jenkinsonb, L.A.Lebel, S.Liras, J.Pandit, B.Samas, F.Vajdos, S.P.Simons, A.Evdokimova, M.Mansour, F.S.Menniti. Small-Molecule Phosphodiesterase Probes: Discovery of Potent and Selective Cns-Penetrable Quinazoline Inhibitors of PDE1 Medchemcomm 2014.
ISSN: ESSN 2040-2511
DOI: 10.1039/C4MD00113C
Page generated: Wed Aug 20 20:48:31 2025

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