sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.880 Å
X-ray
2013-10-16
| Name: | Ribonucleotide reductase (NrdI family protein), putative |
|---|---|
| ID: | A3CR20_STRSV |
| AC: | A3CR20 |
| Organism: | Streptococcus sanguinis |
| Reign: | Bacteria |
| TaxID: | 388919 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 86 % |
| B | 14 % |
| B-Factor: | 25.544 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.427 | 921.375 |
| % Hydrophobic | % Polar |
|---|---|
| 53.85 | 46.15 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 79.46 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -20.703 | 29.4509 | 16.7678 |
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 |
| O3P | OG | SER- 10 | 2.6 | 166.39 | H-Bond (Protein Donor) |
| C7M | CB | LEU- 11 | 4.08 | 0 | Hydrophobic |
| C8M | CB | LEU- 11 | 4.49 | 0 | Hydrophobic |
| O2P | N | LEU- 11 | 2.85 | 148.2 | H-Bond (Protein Donor) |
| O1P | N | SER- 12 | 3.15 | 131.53 | H-Bond (Protein Donor) |
| O2P | N | SER- 12 | 3.16 | 157.45 | H-Bond (Protein Donor) |
| C8M | CB | SER- 12 | 3.95 | 0 | Hydrophobic |
| O4' | ND2 | ASN- 14 | 2.97 | 164.73 | H-Bond (Protein Donor) |
| O1P | N | ASN- 14 | 2.84 | 158.99 | H-Bond (Protein Donor) |
| C5' | CB | ASN- 14 | 4.28 | 0 | Hydrophobic |
| O3P | N | THR- 15 | 2.84 | 162.88 | H-Bond (Protein Donor) |
| O3P | OG1 | THR- 15 | 2.84 | 148.56 | H-Bond (Protein Donor) |
| C5' | CB | PRO- 62 | 3.73 | 0 | Hydrophobic |
| O2' | N | THR- 63 | 3.17 | 136.15 | H-Bond (Protein Donor) |
| O2' | O | THR- 63 | 2.64 | 163.17 | H-Bond (Ligand Donor) |
| C7M | CD1 | TYR- 64 | 4.19 | 0 | Hydrophobic |
| C8M | CE1 | TYR- 64 | 3.73 | 0 | Hydrophobic |
| C2' | CZ | TYR- 64 | 4.45 | 0 | Hydrophobic |
| C5' | CZ | TYR- 64 | 3.89 | 0 | Hydrophobic |
| C8 | CE1 | TYR- 64 | 3.43 | 0 | Hydrophobic |
| O2P | OH | TYR- 64 | 2.64 | 170.28 | H-Bond (Protein Donor) |
| C7M | CD1 | LEU- 79 | 3.87 | 0 | Hydrophobic |
| C4' | CB | SER- 102 | 4.41 | 0 | Hydrophobic |
| O4' | OG | SER- 102 | 2.93 | 147.29 | H-Bond (Ligand Donor) |
| N1 | N | ASN- 104 | 3.24 | 128.28 | H-Bond (Protein Donor) |
| O2 | N | ASN- 104 | 2.99 | 164.27 | H-Bond (Protein Donor) |
| C1' | CB | ASN- 104 | 3.77 | 0 | Hydrophobic |
| C1' | CE2 | PHE- 107 | 3.93 | 0 | Hydrophobic |
| N3 | O | GLN- 110 | 2.87 | 168.28 | H-Bond (Ligand Donor) |
| O2 | N | CYS- 112 | 3.06 | 162.68 | H-Bond (Protein Donor) |
| C8M | C8M | FMN- 201 | 3.95 | 0 | Hydrophobic |
