1.850 Å
X-ray
2011-05-04
Name: | Histone-lysine N-methyltransferase SMYD3 |
---|---|
ID: | SMYD3_HUMAN |
AC: | Q9H7B4 |
Organism: | Homo sapiens |
Reign: | Eukaryota |
TaxID: | 9606 |
EC Number: | 2.1.1.43 |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 28.547 |
---|---|
Number of residues: | 34 |
Including | |
Standard Amino Acids: | 32 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 2 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.866 | 1653.750 |
% Hydrophobic | % Polar |
---|---|
35.51 | 64.49 |
According to VolSite |
HET Code: | SFG |
---|---|
Formula: | C15H24N7O5 |
Molecular weight: | 382.395 g/mol |
DrugBank ID: | DB01910 |
Buried Surface Area: | 70.37 % |
Polar Surface area: | 214.71 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 9 |
H-Bond Donors: | 5 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 1 |
Cationic atoms: | 2 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 7 |
X | Y | Z |
---|---|---|
27.5917 | 51.4414 | 97.5348 |
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 |
N | O | ASN- 16 | 2.87 | 170.24 | H-Bond (Ligand Donor) |
OXT | N | ASN- 16 | 2.82 | 153.5 | H-Bond (Protein Donor) |
O | OH | TYR- 124 | 2.83 | 139.62 | H-Bond (Protein Donor) |
O3' | ND2 | ASN- 132 | 3.06 | 141.54 | H-Bond (Protein Donor) |
NE | OD1 | ASN- 181 | 2.97 | 157.7 | H-Bond (Ligand Donor) |
NE | O | SER- 202 | 2.86 | 151.04 | H-Bond (Ligand Donor) |
N | OD1 | ASN- 205 | 2.72 | 145.6 | H-Bond (Ligand Donor) |
N7 | N | HIS- 206 | 2.81 | 171.59 | H-Bond (Protein Donor) |
N6 | O | HIS- 206 | 2.92 | 150.97 | H-Bond (Ligand Donor) |
NE | OH | TYR- 239 | 3.49 | 122.71 | H-Bond (Ligand Donor) |
C5' | CE2 | TYR- 239 | 4.09 | 0 | Hydrophobic |
C3' | CB | TYR- 257 | 4.15 | 0 | Hydrophobic |
O3' | O | TYR- 257 | 2.72 | 154.78 | H-Bond (Ligand Donor) |
DuAr | DuAr | PHE- 259 | 3.57 | 0 | Aromatic Face/Face |
C2' | CD2 | PHE- 259 | 3.77 | 0 | Hydrophobic |
N6 | O | HOH- 604 | 2.83 | 151.34 | H-Bond (Ligand Donor) |