sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2010-07-19
| 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 | 100 % |
| B-Factor: | 22.082 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.663 | 432.000 |
| % Hydrophobic | % Polar |
|---|---|
| 31.25 | 68.75 |
| According to VolSite | |
| HET Code: | ADN |
|---|---|
| Formula: | C10H13N5O4 |
| Molecular weight: | 267.241 g/mol |
| DrugBank ID: | DB00640 |
| Buried Surface Area: | 53.37 % |
| Polar Surface area: | 139.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -98.2916 | -54.5583 | 2.38826 |
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 |
| O2' | ND2 | ASN- 242 | 3.29 | 157.67 | H-Bond (Protein Donor) |
| N6 | OG | SER- 244 | 2.84 | 174.76 | H-Bond (Ligand Donor) |
| C5' | CB | CYS- 322 | 4.03 | 0 | Hydrophobic |
| C3' | SG | CYS- 322 | 3.64 | 0 | Hydrophobic |
| C5' | CG | PRO- 490 | 4.42 | 0 | Hydrophobic |
| C3' | CG | PRO- 490 | 4.4 | 0 | Hydrophobic |
| C5' | CB | SER- 596 | 3.93 | 0 | Hydrophobic |
