sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2007-11-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.000 | 8.000 | 8.000 | 0.000 | 8.000 | 2 |
| Name: | Disintegrin and metalloproteinase domain-containing protein 17 |
|---|---|
| ID: | ADA17_HUMAN |
| AC: | P78536 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24.86 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 26.601 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.394 | 445.500 |
| % Hydrophobic | % Polar |
|---|---|
| 39.39 | 60.61 |
| According to VolSite | |
| HET Code: | 440 |
|---|---|
| Formula: | C13H16O3S2 |
| Molecular weight: | 284.394 g/mol |
| DrugBank ID: | DB07079 |
| Buried Surface Area: | 73.22 % |
| Polar Surface area: | 90.55 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 0.255667 | 59.6355 | 85.0197 |
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 |
| C2 | CB | LEU- 348 | 4.01 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 348 | 4.43 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 348 | 4.46 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 348 | 4.18 | 0 | Hydrophobic |
| O2 | N | LEU- 348 | 3.06 | 171.8 | H-Bond (Protein Donor) |
| S1 | CD1 | LEU- 350 | 4.23 | 0 | Hydrophobic |
| C6 | CG | GLU- 398 | 3.65 | 0 | Hydrophobic |
| C8 | CB | LEU- 401 | 3.71 | 0 | Hydrophobic |
| C7 | CB | LEU- 401 | 3.75 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 402 | 4.21 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 402 | 4.12 | 0 | Hydrophobic |
| C5 | CB | HIS- 405 | 4.12 | 0 | Hydrophobic |
| C4 | CB | HIS- 405 | 3.85 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 405 | 3.82 | 0 | Aromatic Face/Face |
| C5 | CG2 | VAL- 434 | 4.42 | 0 | Hydrophobic |
| C | CB | ALA- 439 | 4.09 | 0 | Hydrophobic |
| C7 | CB | ALA- 439 | 3.94 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 440 | 4.11 | 0 | Hydrophobic |
