1.890 Å
X-ray
2006-11-27
Name: | Spermidine synthase |
---|---|
ID: | SPEE_HUMAN |
AC: | P19623 |
Organism: | Homo sapiens |
Reign: | Eukaryota |
TaxID: | 9606 |
EC Number: | 2.5.1.16 |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 21.908 |
---|---|
Number of residues: | 28 |
Including | |
Standard Amino Acids: | 27 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 1 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.959 | 702.000 |
% Hydrophobic | % Polar |
---|---|
49.04 | 50.96 |
According to VolSite |
HET Code: | MTA |
---|---|
Formula: | C11H15N5O3S |
Molecular weight: | 297.333 g/mol |
DrugBank ID: | DB02282 |
Buried Surface Area: | 71.37 % |
Polar Surface area: | 144.61 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 8 |
H-Bond Donors: | 3 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 0 |
Cationic atoms: | 0 |
Rule of Five Violation: | 0 |
Rotatable Bonds: | 3 |
X | Y | Z |
---|---|---|
2.952 | 66.7166 | 7.44965 |
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 |
O2' | NE2 | GLN- 49 | 2.9 | 163.19 | H-Bond (Protein Donor) |
CS | CD2 | LEU- 63 | 4.17 | 0 | Hydrophobic |
CS | CD1 | LEU- 65 | 3.9 | 0 | Hydrophobic |
C3' | CD1 | LEU- 65 | 3.7 | 0 | Hydrophobic |
CS | CB | GLN- 70 | 4.13 | 0 | Hydrophobic |
O2' | OE2 | GLU- 124 | 2.69 | 164.05 | H-Bond (Ligand Donor) |
O3' | OE1 | GLU- 124 | 2.57 | 161.16 | H-Bond (Ligand Donor) |
O3' | OE2 | GLU- 124 | 3.23 | 133.5 | H-Bond (Ligand Donor) |
C1' | CG2 | ILE- 125 | 4.36 | 0 | Hydrophobic |
N3 | N | ILE- 125 | 3.43 | 146.32 | H-Bond (Protein Donor) |
CS | CG1 | VAL- 129 | 4.42 | 0 | Hydrophobic |
C3' | CG1 | VAL- 129 | 4.41 | 0 | Hydrophobic |
N6 | OD1 | ASP- 155 | 2.78 | 164.7 | H-Bond (Ligand Donor) |
N1 | N | GLY- 156 | 2.79 | 165.05 | H-Bond (Protein Donor) |
O4' | N | SER- 175 | 3.41 | 133.82 | H-Bond (Protein Donor) |
C5' | CB | SER- 175 | 4.07 | 0 | Hydrophobic |
C2' | CB | SER- 175 | 3.91 | 0 | Hydrophobic |