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
2012-06-05
| Name: | Terminal uridylyltransferase cid1 |
|---|---|
| ID: | CID1_SCHPO |
| AC: | O13833 |
| Organism: | Schizosaccharomyces pombe |
| Reign: | Eukaryota |
| TaxID: | 284812 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.031 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.266 | 648.000 |
| % Hydrophobic | % Polar |
|---|---|
| 42.19 | 57.81 |
| According to VolSite | |
| HET Code: | UTP |
|---|---|
| Formula: | C9H11N2O15P3 |
| Molecular weight: | 480.109 g/mol |
| DrugBank ID: | DB04005 |
| Buried Surface Area: | 55.72 % |
| Polar Surface area: | 299.67 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 15 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -16.0067 | 3.6501 | -7.10007 |
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 |
| C4' | CE2 | PHE- 88 | 3.87 | 0 | Hydrophobic |
| C1' | CE2 | PHE- 88 | 4.01 | 0 | Hydrophobic |
| C2' | CD2 | PHE- 88 | 4.44 | 0 | Hydrophobic |
| O1B | OG | SER- 90 | 2.54 | 171.84 | H-Bond (Protein Donor) |
| O2B | OG | SER- 90 | 3.38 | 122.6 | H-Bond (Protein Donor) |
| C1' | CB | ALA- 168 | 4.24 | 0 | Hydrophobic |
| O2' | OD1 | ASN- 171 | 2.75 | 163.44 | H-Bond (Ligand Donor) |
| O2 | ND2 | ASN- 171 | 2.79 | 148.34 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 193 | 3.03 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 193 | 2.65 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 193 | 2.65 | 148.86 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 197 | 3.01 | 160.82 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 197 | 3.01 | 0 | Ionic (Protein Cationic) |
| O3G | OG | SER- 211 | 3.05 | 167.94 | H-Bond (Protein Donor) |
| O1A | N | TYR- 212 | 3.39 | 153.48 | H-Bond (Protein Donor) |
| C3' | CD1 | TYR- 212 | 3.78 | 0 | Hydrophobic |
| O2A | MG | MG- 402 | 2.23 | 0 | Metal Acceptor |
| O1G | MG | MG- 402 | 2.2 | 0 | Metal Acceptor |
| O3' | O | HOH- 523 | 2.62 | 154.55 | H-Bond (Ligand Donor) |
| O1G | O | HOH- 524 | 2.86 | 140.99 | H-Bond (Protein Donor) |
