sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2012-06-07
| 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: | 23.382 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.180 | 313.875 |
| % Hydrophobic | % Polar |
|---|---|
| 51.61 | 48.39 |
| According to VolSite | |
| HET Code: | 3AT |
|---|---|
| Formula: | C10H12N5O12P3 |
| Molecular weight: | 487.150 g/mol |
| DrugBank ID: | DB01860 |
| Buried Surface Area: | 49.24 % |
| Polar Surface area: | 299.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -16.2755 | 4.29473 | -7.13577 |
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' | CD2 | PHE- 88 | 4.07 | 0 | Hydrophobic |
| O1G | OG | SER- 90 | 3.02 | 154.3 | H-Bond (Protein Donor) |
| C2' | CB | ASN- 171 | 4.36 | 0 | Hydrophobic |
| O2' | ND2 | ASN- 171 | 2.97 | 172.67 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 193 | 2.95 | 165.6 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 193 | 2.95 | 0 | Ionic (Protein Cationic) |
| O1B | NZ | LYS- 193 | 3.87 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 197 | 3.68 | 0 | Ionic (Protein Cationic) |
| O2G | OG | SER- 211 | 2.92 | 158.42 | H-Bond (Protein Donor) |
| C5' | CB | TYR- 212 | 4.45 | 0 | Hydrophobic |
| C3' | CD1 | TYR- 212 | 3.67 | 0 | Hydrophobic |
| C2' | CD2 | TYR- 212 | 4.23 | 0 | Hydrophobic |
| N1 | NE2 | HIS- 336 | 2.58 | 128.71 | H-Bond (Protein Donor) |
| O3G | MG | MG- 402 | 2.21 | 0 | Metal Acceptor |
| O2B | MG | MG- 402 | 2.2 | 0 | Metal Acceptor |
| O2A | MG | MG- 402 | 2.21 | 0 | Metal Acceptor |
