sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.170 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 | 78 % |
| B | 22 % |
| B-Factor: | 35.925 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.196 | 1532.250 |
| % Hydrophobic | % Polar |
|---|---|
| 50.88 | 49.12 |
| According to VolSite | |
| HET Code: | LPO |
|---|---|
| Formula: | C33H39Cl3N3O5 |
| Molecular weight: | 664.039 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.75 % |
| Polar Surface area: | 97.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 29.5704 | -7.74727 | 1.3838 |
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 |
| C35 | CG | GLN- 19 | 3.9 | 0 | Hydrophobic |
| C42 | CB | GLN- 19 | 4.05 | 0 | Hydrophobic |
| O43 | N | TYR- 20 | 2.97 | 163.34 | H-Bond (Protein Donor) |
| C44 | CD2 | TYR- 20 | 4.46 | 0 | Hydrophobic |
| C38 | CG1 | VAL- 36 | 3.88 | 0 | Hydrophobic |
| C39 | CB | VAL- 36 | 3.8 | 0 | Hydrophobic |
| C42 | CG2 | VAL- 36 | 3.61 | 0 | Hydrophobic |
| C44 | CG1 | VAL- 36 | 4.3 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 38 | 3.41 | 121.33 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 38 | 3.01 | 167.74 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 38 | 3.41 | 0 | Ionic (Ligand Cationic) |
| N3 | OD1 | ASP- 38 | 3.01 | 0 | Ionic (Ligand Cationic) |
| C38 | CB | ASP- 38 | 3.89 | 0 | Hydrophobic |
| C1 | CB | SER- 41 | 3.97 | 0 | Hydrophobic |
| CL27 | CB | TRP- 45 | 3.68 | 0 | Hydrophobic |
| C18 | CB | TRP- 45 | 3.95 | 0 | Hydrophobic |
| C22 | CG | PRO- 47 | 4.22 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 81 | 4.33 | 0 | Hydrophobic |
| C15 | CE2 | TYR- 83 | 3.35 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 88 | 4.04 | 0 | Hydrophobic |
| CL27 | CG2 | VAL- 111 | 3.37 | 0 | Hydrophobic |
| C18 | CE | MET- 114 | 3.81 | 0 | Hydrophobic |
| C22 | SD | MET- 114 | 3.99 | 0 | Hydrophobic |
| CL27 | CE | MET- 114 | 4.01 | 0 | Hydrophobic |
| C21 | CE | MET- 114 | 3.84 | 0 | Hydrophobic |
| CL40 | CG | PRO- 118 | 3.83 | 0 | Hydrophobic |
| C18 | CE1 | PHE- 119 | 4.46 | 0 | Hydrophobic |
| CL26 | CE1 | PHE- 119 | 3.39 | 0 | Hydrophobic |
| CL40 | CD1 | PHE- 119 | 3.63 | 0 | Hydrophobic |
| C14 | CZ | PHE- 119 | 3.43 | 0 | Hydrophobic |
| C24 | CB | ALA- 122 | 4.18 | 0 | Hydrophobic |
| C28 | CB | ALA- 122 | 3.82 | 0 | Hydrophobic |
| CL26 | CE2 | PHE- 124 | 3.86 | 0 | Hydrophobic |
| C39 | CE2 | PHE- 124 | 3.86 | 0 | Hydrophobic |
| CL40 | CZ | PHE- 124 | 4.34 | 0 | Hydrophobic |
| C42 | CE1 | PHE- 124 | 4.34 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 127 | 4.22 | 0 | Hydrophobic |
| CL26 | CG1 | VAL- 127 | 4.33 | 0 | Hydrophobic |
| C38 | CG2 | VAL- 127 | 4.15 | 0 | Hydrophobic |
| C39 | CB | VAL- 127 | 4.4 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 127 | 3.73 | 0 | Hydrophobic |
| N3 | OD1 | ASP- 226 | 3.18 | 0 | Ionic (Ligand Cationic) |
| N3 | OD2 | ASP- 226 | 2.85 | 0 | Ionic (Ligand Cationic) |
| N3 | OD2 | ASP- 226 | 2.85 | 142.97 | H-Bond (Ligand Donor) |
| C41 | CB | SER- 230 | 4.46 | 0 | Hydrophobic |
