sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2007-01-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.100 | 7.100 | 7.100 | 0.000 | 7.100 | 1 |
| Name: | Geranylgeranyl pyrophosphate synthase |
|---|---|
| ID: | GGPPS_YEAST |
| AC: | Q12051 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 39.580 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.698 | 519.750 |
| % Hydrophobic | % Polar |
|---|---|
| 51.30 | 48.70 |
| According to VolSite | |
| HET Code: | B75 |
|---|---|
| Formula: | C24H19NO9P2S |
| Molecular weight: | 559.421 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.07 % |
| Polar Surface area: | 220.78 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 24.1491 | 29.4111 | 33.8896 |
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 |
| CAX | CG | ARG- 44 | 3.58 | 0 | Hydrophobic |
| CAL | CD2 | LEU- 47 | 3.78 | 0 | Hydrophobic |
| CAM | CG1 | ILE- 48 | 3.5 | 0 | Hydrophobic |
| CAT | CG1 | VAL- 69 | 3.69 | 0 | Hydrophobic |
| CAY | CD2 | LEU- 77 | 3.92 | 0 | Hydrophobic |
| CAN | CB | ASP- 80 | 4.19 | 0 | Hydrophobic |
| CAY | CB | ASP- 80 | 4.43 | 0 | Hydrophobic |
| OAF | NH2 | ARG- 89 | 3.39 | 142.84 | H-Bond (Protein Donor) |
| OAA | NH2 | ARG- 89 | 3.39 | 130.34 | H-Bond (Protein Donor) |
| OAA | NH1 | ARG- 89 | 2.82 | 155.01 | H-Bond (Protein Donor) |
| OAA | CZ | ARG- 89 | 3.54 | 0 | Ionic (Protein Cationic) |
| CAP | CD1 | LEU- 143 | 3.93 | 0 | Hydrophobic |
| OAI | NZ | LYS- 174 | 3.1 | 135.34 | H-Bond (Protein Donor) |
| OAI | NZ | LYS- 174 | 3.1 | 0 | Ionic (Protein Cationic) |
| CAJ | CG | LYS- 174 | 4.02 | 0 | Hydrophobic |
| CAQ | CG2 | THR- 175 | 4.05 | 0 | Hydrophobic |
| CAR | CB | LEU- 178 | 4.32 | 0 | Hydrophobic |
| CBB | CD1 | LEU- 178 | 4.45 | 0 | Hydrophobic |
| CAQ | CD1 | LEU- 178 | 4.17 | 0 | Hydrophobic |
| CAK | CB | LEU- 178 | 3.56 | 0 | Hydrophobic |
| CAS | CB | PHE- 179 | 4.46 | 0 | Hydrophobic |
| CAU | CG | PHE- 179 | 3.26 | 0 | Hydrophobic |
| CAS | CB | THR- 182 | 3.78 | 0 | Hydrophobic |
| CAL | CG2 | THR- 182 | 3.45 | 0 | Hydrophobic |
| OAG | OD2 | ASP- 214 | 2.66 | 161.59 | H-Bond (Protein Donor) |
| OAE | OD2 | ASP- 214 | 3.3 | 167.6 | H-Bond (Ligand Donor) |
| OAH | NZ | LYS- 238 | 3.85 | 0 | Ionic (Protein Cationic) |
| OAI | NZ | LYS- 238 | 3.93 | 0 | Ionic (Protein Cationic) |
| OAB | O | HOH- 667 | 2.93 | 179.98 | H-Bond (Protein Donor) |
| OAF | MG | MG- 1303 | 1.83 | 0 | Metal Acceptor |
| OAH | MG | MG- 1303 | 2 | 0 | Metal Acceptor |
| OAH | MG | MG- 1304 | 2.02 | 0 | Metal Acceptor |
