sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2009-12-10
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.640 | 7.640 | 7.640 | 0.000 | 7.640 | 1 |
| 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: | 26.001 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.254 | 388.125 |
| % Hydrophobic | % Polar |
|---|---|
| 39.13 | 60.87 |
| According to VolSite | |
| HET Code: | 724 |
|---|---|
| Formula: | C13H14N4O4 |
| Molecular weight: | 290.275 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.29 % |
| Polar Surface area: | 99.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 6.85567 | 9.73252 | 25.0175 |
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 |
| C11 | CG2 | THR- 347 | 4.5 | 0 | Hydrophobic |
| C12 | CG2 | THR- 347 | 4.19 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 348 | 4.14 | 0 | Hydrophobic |
| O19 | N | LEU- 348 | 2.76 | 163.68 | H-Bond (Protein Donor) |
| N7 | O | GLY- 349 | 2.81 | 163.47 | H-Bond (Ligand Donor) |
| O19 | N | GLY- 349 | 3.05 | 158.86 | H-Bond (Protein Donor) |
| C11 | CD1 | LEU- 350 | 3.75 | 0 | Hydrophobic |
| C21 | CB | LEU- 401 | 3.88 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 402 | 4.5 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 402 | 4.21 | 0 | Hydrophobic |
| N4 | NE2 | HIS- 405 | 3.27 | 122.18 | H-Bond (Ligand Donor) |
| C21 | CB | HIS- 405 | 4.02 | 0 | Hydrophobic |
| C17 | CB | HIS- 405 | 3.97 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 405 | 3.78 | 0 | Aromatic Face/Face |
| N4 | NE2 | HIS- 415 | 3.11 | 146.2 | H-Bond (Ligand Donor) |
| N2 | O | PRO- 437 | 2.87 | 123.77 | H-Bond (Ligand Donor) |
| C21 | CB | ALA- 439 | 3.97 | 0 | Hydrophobic |
| C16 | CB | ALA- 439 | 3.65 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 440 | 4.26 | 0 | Hydrophobic |
