sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2005-06-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.700 | 5.700 | 5.700 | 0.000 | 5.700 | 1 |
| Name: | Indolethylamine N-methyltransferase |
|---|---|
| ID: | INMT_HUMAN |
| AC: | O95050 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.1.1.49 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 10.296 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.872 | 327.375 |
| % Hydrophobic | % Polar |
|---|---|
| 59.79 | 40.21 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 81.45 % |
| 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 |
|---|---|---|
| 21.7085 | 45.0289 | 7.07912 |
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 |
| C3' | CE2 | TYR- 11 | 4.37 | 0 | Hydrophobic |
| C2' | CD2 | TYR- 11 | 3.74 | 0 | Hydrophobic |
| SD | CZ | PHE- 15 | 4.43 | 0 | Hydrophobic |
| C3' | CZ | PHE- 15 | 4.19 | 0 | Hydrophobic |
| SD | CZ | TYR- 20 | 3.5 | 0 | Hydrophobic |
| CG | CZ | TYR- 20 | 3.96 | 0 | Hydrophobic |
| OXT | OH | TYR- 20 | 2.67 | 174.25 | H-Bond (Protein Donor) |
| OXT | OH | TYR- 25 | 2.65 | 129.34 | H-Bond (Protein Donor) |
| N | O | GLY- 63 | 2.71 | 164.04 | H-Bond (Ligand Donor) |
| O | OH | TYR- 69 | 2.6 | 134.43 | H-Bond (Protein Donor) |
| O3' | OD1 | ASP- 85 | 2.74 | 153.89 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 85 | 2.63 | 144.1 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 85 | 3.44 | 136.9 | H-Bond (Ligand Donor) |
| O2' | OG1 | THR- 87 | 2.8 | 164.83 | H-Bond (Protein Donor) |
| N6 | OD1 | ASP- 142 | 3.04 | 155.36 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 143 | 3.06 | 161.03 | H-Bond (Protein Donor) |
| N | O | LEU- 163 | 2.74 | 156.88 | H-Bond (Ligand Donor) |
| CG | CB | LEU- 164 | 4.08 | 0 | Hydrophobic |
| CG | CB | ALA- 165 | 4.37 | 0 | Hydrophobic |
| C1' | CB | ALA- 165 | 4.39 | 0 | Hydrophobic |
| C4' | CB | ALA- 165 | 3.73 | 0 | Hydrophobic |
| C5' | SG | CYS- 168 | 3.96 | 0 | Hydrophobic |
