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
2006-08-21
| 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: | 12.724 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.320 | 448.875 |
| % Hydrophobic | % Polar |
|---|---|
| 39.85 | 60.15 |
| According to VolSite | |
| HET Code: | INN |
|---|---|
| Formula: | C19H38N5O5 |
| Molecular weight: | 416.536 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.39 % |
| Polar Surface area: | 164.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 6 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -3.34572 | 39.5843 | 49.7018 |
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 |
| N2 | O | GLY- 346 | 2.92 | 160.36 | H-Bond (Ligand Donor) |
| O1 | N | LEU- 348 | 2.81 | 159.15 | H-Bond (Protein Donor) |
| C12 | CD1 | LEU- 348 | 4.34 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 348 | 4.02 | 0 | Hydrophobic |
| N | O | GLY- 349 | 3.1 | 165.45 | H-Bond (Ligand Donor) |
| O3 | OH | TYR- 390 | 2.7 | 171.86 | H-Bond (Protein Donor) |
| C12 | CE1 | TYR- 390 | 4.22 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 402 | 4.01 | 0 | Hydrophobic |
| C3 | CB | HIS- 405 | 4.12 | 0 | Hydrophobic |
| O4 | OE1 | GLU- 406 | 2.73 | 157.23 | H-Bond (Protein Donor) |
| N1 | O | PRO- 437 | 3.3 | 168.38 | H-Bond (Ligand Donor) |
| O2 | N | ALA- 439 | 2.89 | 163.13 | H-Bond (Protein Donor) |
| C12 | CB | ALA- 439 | 4.3 | 0 | Hydrophobic |
| C2 | CB | ALA- 439 | 3.9 | 0 | Hydrophobic |
| O | ZN | ZN- 802 | 2.14 | 0 | Metal Acceptor |
| O4 | ZN | ZN- 802 | 2.08 | 0 | Metal Acceptor |
| O4 | O | HOH- 958 | 2.65 | 147.49 | H-Bond (Protein Donor) |
