sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2004-09-23
| Name: | Vitamin B12-dependent ribonucleotide reductase |
|---|---|
| ID: | O33839_THEMT |
| AC: | O33839 |
| Organism: | Thermotoga maritima |
| Reign: | Bacteria |
| TaxID: | 2336 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 26 % |
| B | 74 % |
| B-Factor: | 53.745 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.192 | 371.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.45 | 54.55 |
| According to VolSite | |
| HET Code: | DTP |
|---|---|
| Formula: | C10H12N5O12P3 |
| Molecular weight: | 487.150 g/mol |
| DrugBank ID: | DB03222 |
| Buried Surface Area: | 64.05 % |
| 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 |
|---|---|---|
| -77.081 | -64.8486 | -13.826 |
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 |
| O1B | NE2 | HIS- 127 | 2.78 | 141.12 | H-Bond (Protein Donor) |
| O3' | OD1 | ASP- 141 | 2.58 | 163.54 | H-Bond (Ligand Donor) |
| O2A | N | ILE- 143 | 3.39 | 178.23 | H-Bond (Protein Donor) |
| C2' | CD1 | ILE- 143 | 3.82 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 146 | 3.91 | 0 | Hydrophobic |
| O2A | NZ | LYS- 158 | 3.95 | 0 | Ionic (Protein Cationic) |
| O1G | CZ | ARG- 171 | 3.76 | 0 | Ionic (Protein Cationic) |
| O1G | NH1 | ARG- 171 | 2.94 | 157.89 | H-Bond (Protein Donor) |
| O2G | NH2 | ARG- 171 | 3.49 | 144.25 | H-Bond (Protein Donor) |
| C4' | CD | ARG- 171 | 3.97 | 0 | Hydrophobic |
| C4' | CG1 | VAL- 177 | 4.47 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 177 | 3.85 | 0 | Hydrophobic |
| C1' | CB | ALA- 184 | 3.82 | 0 | Hydrophobic |
| N3 | N | SER- 185 | 3.24 | 120.6 | H-Bond (Protein Donor) |
| C2' | CZ | PHE- 190 | 3.72 | 0 | Hydrophobic |
| N6 | O | LYS- 202 | 3.19 | 136.36 | H-Bond (Ligand Donor) |
| O2G | MG | MG- 1005 | 2.17 | 0 | Metal Acceptor |
| O1A | MG | MG- 1005 | 2.07 | 0 | Metal Acceptor |
| O3' | O | HOH- 1017 | 3.4 | 158.29 | H-Bond (Protein Donor) |
