sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2008-08-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.750 | 9.750 | 9.750 | 0.000 | 9.750 | 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 |
|---|---|
| B | 100 % |
| B-Factor: | 25.932 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.635 | 702.000 |
| % Hydrophobic | % Polar |
|---|---|
| 37.02 | 62.98 |
| According to VolSite | |
| HET Code: | 615 |
|---|---|
| Formula: | C28H25N3O4 |
| Molecular weight: | 467.516 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.47 % |
| Polar Surface area: | 114.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 49.8335 | 30.0895 | 43.8197 |
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 |
| O2 | ZN | ZN- 2 | 1.94 | 0 | Metal Acceptor |
| O4 | ZN | ZN- 2 | 2.12 | 0 | Metal Acceptor |
| N3 | O | GLY- 346 | 3.22 | 155.7 | H-Bond (Ligand Donor) |
| O1 | N | LEU- 348 | 2.61 | 169.37 | H-Bond (Protein Donor) |
| C27 | CD1 | LEU- 348 | 3.72 | 0 | Hydrophobic |
| N2 | O | GLY- 349 | 3.16 | 163.9 | H-Bond (Ligand Donor) |
| C27 | CB | GLU- 398 | 3.61 | 0 | Hydrophobic |
| C26 | CG | GLU- 398 | 3.52 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 401 | 4.22 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 401 | 4.28 | 0 | Hydrophobic |
| C13 | CB | LEU- 401 | 3.68 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 402 | 4.26 | 0 | Hydrophobic |
| C28 | CG2 | VAL- 402 | 3.91 | 0 | Hydrophobic |
| C10 | CB | HIS- 405 | 3.83 | 0 | Hydrophobic |
| C7 | CB | HIS- 405 | 3.71 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 405 | 3.62 | 0 | Aromatic Face/Face |
| C18 | CB | LYS- 432 | 4.07 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 434 | 4.1 | 0 | Hydrophobic |
| C17 | CB | TYR- 436 | 3.81 | 0 | Hydrophobic |
| C13 | CB | ALA- 439 | 3.88 | 0 | Hydrophobic |
| C28 | CB | ALA- 439 | 3.82 | 0 | Hydrophobic |
| C9 | CB | ALA- 439 | 3.57 | 0 | Hydrophobic |
| C18 | CB | ASN- 447 | 3.83 | 0 | Hydrophobic |
