sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2004-07-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.600 | 4.600 | 4.600 | 0.000 | 4.600 | 1 |
| Name: | Pancreatic alpha-amylase |
|---|---|
| ID: | AMYP_HUMAN |
| AC: | P04746 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.267 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.722 | 543.375 |
| % Hydrophobic | % Polar |
|---|---|
| 39.13 | 60.87 |
| According to VolSite | |
| HET Code: | LM2 |
|---|---|
| Formula: | C19H35N2O15 |
| Molecular weight: | 531.486 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.06 % |
| Polar Surface area: | 274.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 15 |
| H-Bond Donors: | 12 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 13.8292 | 15.4557 | 39.189 |
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 |
| CB2 | CH2 | TRP- 58 | 3.59 | 0 | Hydrophobic |
| CB5 | CB | TRP- 59 | 4.08 | 0 | Hydrophobic |
| CB6 | CE3 | TRP- 59 | 4.4 | 0 | Hydrophobic |
| CD1 | CE3 | TRP- 59 | 3.61 | 0 | Hydrophobic |
| CD2 | CH2 | TRP- 59 | 3.86 | 0 | Hydrophobic |
| CB2 | CB | TRP- 59 | 3.57 | 0 | Hydrophobic |
| CB4 | CB | TRP- 59 | 3.86 | 0 | Hydrophobic |
| OB6 | O | TRP- 59 | 2.51 | 150.08 | H-Bond (Ligand Donor) |
| CA2 | CD1 | TYR- 62 | 4.3 | 0 | Hydrophobic |
| CA6 | CB | TYR- 62 | 4.04 | 0 | Hydrophobic |
| CB1 | CB | TYR- 62 | 4.23 | 0 | Hydrophobic |
| CA4 | CG | TYR- 62 | 3.99 | 0 | Hydrophobic |
| CB6 | CB | TYR- 62 | 4.05 | 0 | Hydrophobic |
| CB6 | CG | GLN- 63 | 3.5 | 0 | Hydrophobic |
| OB6 | NE2 | GLN- 63 | 2.81 | 164.71 | H-Bond (Protein Donor) |
| CA6 | CD2 | LEU- 162 | 4.01 | 0 | Hydrophobic |
| CA6 | CD2 | LEU- 165 | 3.58 | 0 | Hydrophobic |
| CB6 | CD2 | LEU- 165 | 4.4 | 0 | Hydrophobic |
| CD6 | CD1 | LEU- 165 | 3.43 | 0 | Hydrophobic |
| OA2 | NH2 | ARG- 195 | 2.9 | 141.9 | H-Bond (Protein Donor) |
| OA6 | OD2 | ASP- 197 | 2.83 | 135.74 | H-Bond (Ligand Donor) |
| OA7 | OE1 | GLU- 233 | 2.52 | 125.78 | H-Bond (Ligand Donor) |
| OA3 | NE2 | HIS- 299 | 3.08 | 144.77 | H-Bond (Protein Donor) |
| OA3 | OD1 | ASP- 300 | 2.62 | 150.87 | H-Bond (Ligand Donor) |
| OB2 | ND1 | HIS- 305 | 2.79 | 158.92 | H-Bond (Protein Donor) |
| OD6 | O | HOH- 611 | 2.71 | 179.96 | H-Bond (Protein Donor) |
