sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.280 Å
X-ray
2001-08-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.740 | 4.860 | 4.860 | 0.120 | 4.980 | 2 |
| Name: | Histamine N-methyltransferase |
|---|---|
| ID: | HNMT_HUMAN |
| AC: | P50135 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.1.1.8 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.699 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.067 | 1549.125 |
| % Hydrophobic | % Polar |
|---|---|
| 57.95 | 42.05 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 58.58 % |
| Polar Surface area: | 212.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 39.9634 | -26.1324 | 3.05562 |
Image generated by PoseView
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 | GLY- 60 | 2.81 | 155.45 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 89 | 3.27 | 147.74 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 89 | 2.58 | 146.4 | H-Bond (Ligand Donor) |
| O2' | OE1 | GLU- 89 | 3.46 | 131.12 | H-Bond (Ligand Donor) |
| C1' | CG | PRO- 90 | 4.39 | 0 | Hydrophobic |
| O3' | NE2 | GLN- 94 | 2.96 | 172.64 | H-Bond (Protein Donor) |
| N1 | N | SER- 120 | 2.88 | 155.31 | H-Bond (Protein Donor) |
| N | O | ILE- 142 | 2.92 | 144.2 | H-Bond (Ligand Donor) |
| CG | CB | GLN- 143 | 3.81 | 0 | Hydrophobic |
| C5' | CB | MET- 144 | 4.11 | 0 | Hydrophobic |
| C5' | CE1 | TYR- 147 | 3.59 | 0 | Hydrophobic |
| N6 | O | TYR- 147 | 3.38 | 128 | H-Bond (Ligand Donor) |
| N6 | O | HOH- 773 | 2.7 | 169.46 | H-Bond (Ligand Donor) |
| OXT | O | HOH- 775 | 2.74 | 145.49 | H-Bond (Protein Donor) |
