sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.240 Å
X-ray
2006-10-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.100 | 7.100 | 7.100 | 0.000 | 7.100 | 1 |
| Name: | Renin |
|---|---|
| ID: | RENI_HUMAN |
| AC: | P00797 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.23.15 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 43.352 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.394 | 1107.000 |
| % Hydrophobic | % Polar |
|---|---|
| 42.68 | 57.32 |
| According to VolSite | |
| HET Code: | LIX |
|---|---|
| Formula: | C32H38N6O5S |
| Molecular weight: | 618.746 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.3 % |
| Polar Surface area: | 157.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -24.5677 | -2.24764 | -10.4826 |
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 |
| C17 | CG | GLN- 14 | 4.16 | 0 | Hydrophobic |
| O1 | N | TYR- 15 | 3.36 | 166.6 | H-Bond (Protein Donor) |
| C19 | CB | TYR- 15 | 4.04 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 31 | 3.49 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 31 | 4.24 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 31 | 3.85 | 0 | Hydrophobic |
| C6 | CB | ASP- 33 | 4.32 | 0 | Hydrophobic |
| N2 | OD1 | ASP- 33 | 2.63 | 168.38 | H-Bond (Ligand Donor) |
| N4 | OD1 | ASP- 33 | 3.31 | 128.93 | H-Bond (Ligand Donor) |
| N4 | OD2 | ASP- 33 | 3.01 | 128.37 | H-Bond (Ligand Donor) |
| C4 | CB | TYR- 78 | 4.3 | 0 | Hydrophobic |
| C5 | CE2 | TYR- 78 | 3.89 | 0 | Hydrophobic |
| C7 | CB | TYR- 78 | 4.24 | 0 | Hydrophobic |
| C20 | CB | SER- 79 | 4.44 | 0 | Hydrophobic |
| C21 | CG2 | THR- 80 | 4.14 | 0 | Hydrophobic |
| C29 | CG2 | THR- 80 | 3.61 | 0 | Hydrophobic |
| O5 | OG1 | THR- 80 | 2.98 | 150.21 | H-Bond (Protein Donor) |
| C8 | CG | PRO- 113 | 4.13 | 0 | Hydrophobic |
| C22 | CB | PRO- 113 | 4.02 | 0 | Hydrophobic |
| C13 | CB | LEU- 116 | 4 | 0 | Hydrophobic |
| C13 | CB | ALA- 117 | 4.12 | 0 | Hydrophobic |
| C13 | CE1 | PHE- 119 | 4.48 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 119 | 3.83 | 0 | Hydrophobic |
| C14 | CZ | PHE- 119 | 4.48 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 122 | 3.66 | 0 | Hydrophobic |
| C19 | CZ | TYR- 157 | 4.35 | 0 | Hydrophobic |
| N4 | OD1 | ASP- 221 | 3.14 | 134.49 | H-Bond (Ligand Donor) |
| C20 | CB | ALA- 224 | 4.47 | 0 | Hydrophobic |
| O4 | N | SER- 225 | 3.13 | 160.09 | H-Bond (Protein Donor) |
| C31 | CB | SER- 225 | 3.74 | 0 | Hydrophobic |
| C28 | CB | PHE- 248 | 3.72 | 0 | Hydrophobic |
| O3 | O | HOH- 608 | 2.75 | 152.61 | H-Bond (Protein Donor) |
