2.100 Å
X-ray
2008-07-28
Name: | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A |
---|---|
ID: | PDE9A_HUMAN |
AC: | O76083 |
Organism: | Homo sapiens |
Reign: | Eukaryota |
TaxID: | 9606 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 35.498 |
---|---|
Number of residues: | 33 |
Including | |
Standard Amino Acids: | 30 |
Non Standard Amino Acids: | 2 |
Water Molecules: | 1 |
Cofactors: | |
Metals: | ZN MG |
Ligandability | Volume (Å3) |
---|---|
1.077 | 840.375 |
% Hydrophobic | % Polar |
---|---|
53.01 | 46.99 |
According to VolSite |
HET Code: | PCG |
---|---|
Formula: | C10H11N5O7P |
Molecular weight: | 344.197 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 52.63 % |
Polar Surface area: | 183.16 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 10 |
H-Bond Donors: | 3 |
Rings: | 4 |
Aromatic rings: | 1 |
Anionic atoms: | 1 |
Cationic atoms: | 0 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 1 |
X | Y | Z |
---|---|---|
78.1404 | 51.0488 | 41.2877 |
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
Ligand | Protein | Interaction | |||
---|---|---|---|---|---|
Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
O1A | NE2 | HIS- 252 | 2.81 | 161.26 | H-Bond (Ligand Donor) |
C5' | CG | MET- 365 | 3.33 | 0 | Hydrophobic |
C5' | CG2 | ILE- 403 | 3.66 | 0 | Hydrophobic |
C2' | CD1 | LEU- 420 | 3.96 | 0 | Hydrophobic |
C2' | CZ | TYR- 424 | 4.36 | 0 | Hydrophobic |
N2 | O | ALA- 452 | 3.4 | 136.06 | H-Bond (Ligand Donor) |
O6 | NE2 | GLN- 453 | 2.92 | 175.12 | H-Bond (Protein Donor) |
N1 | OE1 | GLN- 453 | 2.64 | 164.42 | H-Bond (Ligand Donor) |
N2 | OE1 | GLN- 453 | 3.2 | 129.47 | H-Bond (Ligand Donor) |
C1' | CZ | PHE- 456 | 3.8 | 0 | Hydrophobic |
N7 | O | HOH- 1050 | 2.9 | 179.96 | H-Bond (Protein Donor) |