sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2010-08-05
| 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 | 79 % |
| B | 21 % |
| B-Factor: | 33.449 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.367 | 1404.000 |
| % Hydrophobic | % Polar |
|---|---|
| 52.64 | 47.36 |
| According to VolSite | |
| HET Code: | LPQ |
|---|---|
| Formula: | C34H41Cl3N4O3 |
| Molecular weight: | 660.073 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.21 % |
| Polar Surface area: | 84.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 29.776 | -7.14741 | 1.29764 |
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 |
| C34 | CG | GLN- 19 | 4.12 | 0 | Hydrophobic |
| C40 | CG1 | VAL- 36 | 3.76 | 0 | Hydrophobic |
| C41 | CB | VAL- 36 | 3.95 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 38 | 3.02 | 147 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 38 | 3.12 | 148.02 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 38 | 3.02 | 0 | Ionic (Ligand Cationic) |
| N3 | OD1 | ASP- 38 | 3.12 | 0 | Ionic (Ligand Cationic) |
| C40 | CB | ASP- 38 | 4.11 | 0 | Hydrophobic |
| C1 | CB | SER- 41 | 4.16 | 0 | Hydrophobic |
| CL26 | CB | TRP- 45 | 3.96 | 0 | Hydrophobic |
| C18 | CB | TRP- 45 | 3.91 | 0 | Hydrophobic |
| C22 | CG | PRO- 47 | 4.32 | 0 | Hydrophobic |
| CL26 | CG | PRO- 47 | 4.38 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 81 | 3.88 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 81 | 4.3 | 0 | Hydrophobic |
| C12 | CE2 | TYR- 83 | 3.43 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 88 | 4.16 | 0 | Hydrophobic |
| CL26 | CG2 | VAL- 111 | 3.46 | 0 | Hydrophobic |
| C18 | CE | MET- 114 | 3.92 | 0 | Hydrophobic |
| CL26 | CE | MET- 114 | 3.56 | 0 | Hydrophobic |
| C21 | CE | MET- 114 | 3.39 | 0 | Hydrophobic |
| C35 | CB | PRO- 118 | 4.39 | 0 | Hydrophobic |
| CL37 | CG | PRO- 118 | 4.06 | 0 | Hydrophobic |
| C18 | CE1 | PHE- 119 | 4.02 | 0 | Hydrophobic |
| CL27 | CE1 | PHE- 119 | 3.94 | 0 | Hydrophobic |
| C28 | CB | PHE- 119 | 4.49 | 0 | Hydrophobic |
| CL37 | CD1 | PHE- 119 | 3.4 | 0 | Hydrophobic |
| C24 | CB | ALA- 122 | 4.32 | 0 | Hydrophobic |
| C28 | CB | ALA- 122 | 3.66 | 0 | Hydrophobic |
| C35 | CB | ALA- 122 | 4.21 | 0 | Hydrophobic |
| CL37 | CB | ALA- 122 | 4.13 | 0 | Hydrophobic |
| CL27 | CE2 | PHE- 124 | 3.94 | 0 | Hydrophobic |
| CL37 | CZ | PHE- 124 | 4.29 | 0 | Hydrophobic |
| C41 | CZ | PHE- 124 | 3.74 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 127 | 4.32 | 0 | Hydrophobic |
| CL27 | CG1 | VAL- 127 | 4.01 | 0 | Hydrophobic |
| C40 | CG2 | VAL- 127 | 4.34 | 0 | Hydrophobic |
| C41 | CB | VAL- 127 | 4.45 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 127 | 3.62 | 0 | Hydrophobic |
| N3 | OD1 | ASP- 226 | 3.09 | 128.51 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 226 | 2.86 | 154.46 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 226 | 3.09 | 0 | Ionic (Ligand Cationic) |
| N3 | OD2 | ASP- 226 | 2.86 | 0 | Ionic (Ligand Cationic) |
| C44 | CB | ALA- 229 | 4.11 | 0 | Hydrophobic |
| C43 | CB | SER- 230 | 3.84 | 0 | Hydrophobic |
| C43 | CD2 | TYR- 231 | 4.43 | 0 | Hydrophobic |
