sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2015-05-06
| Name: | Putative oxidoreductase molybdopterin-binding subunit |
|---|---|
| ID: | Q96Y29_SULTO |
| AC: | Q96Y29 |
| Organism: | Sulfolobus tokodaii |
| Reign: | Archaea |
| TaxID: | 273063 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 92 % |
| C | 8 % |
| B-Factor: | 22.053 |
|---|---|
| Number of residues: | 65 |
| Including | |
| Standard Amino Acids: | 61 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.914 | 658.125 |
| % Hydrophobic | % Polar |
|---|---|
| 49.23 | 50.77 |
| According to VolSite | |
| HET Code: | MCN |
|---|---|
| Formula: | C19H20N8O13P2S2 |
| Molecular weight: | 694.485 g/mol |
| DrugBank ID: | DB03300 |
| Buried Surface Area: | 88.57 % |
| Polar Surface area: | 420.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 7 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 90.9021 | 56.521 | 21.3803 |
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 |
| N2' | OE1 | GLN- 105 | 2.8 | 158.82 | H-Bond (Ligand Donor) |
| O4' | N | ALA- 214 | 2.75 | 130.57 | H-Bond (Protein Donor) |
| C6' | CD1 | PHE- 215 | 4.04 | 0 | Hydrophobic |
| O4' | N | PHE- 215 | 2.94 | 139.38 | H-Bond (Protein Donor) |
| C6' | CG | ARG- 332 | 4.08 | 0 | Hydrophobic |
| O3' | O | GLN- 444 | 2.72 | 167.44 | H-Bond (Ligand Donor) |
| C5' | CB | GLN- 444 | 4.49 | 0 | Hydrophobic |
| C7 | CG | GLN- 444 | 4.13 | 0 | Hydrophobic |
| C10 | CG | GLN- 444 | 4.11 | 0 | Hydrophobic |
| O9' | NE2 | GLN- 444 | 3.2 | 147.41 | H-Bond (Protein Donor) |
| O2B | OD2 | ASP- 446 | 2.78 | 150.51 | H-Bond (Protein Donor) |
| C2D | CB | ALA- 449 | 4.42 | 0 | Hydrophobic |
| C10 | CG2 | THR- 481 | 3.8 | 0 | Hydrophobic |
| O1B | N | ARG- 485 | 3.28 | 121.19 | H-Bond (Protein Donor) |
| O1B | N | THR- 486 | 2.91 | 151.68 | H-Bond (Protein Donor) |
| O1B | OG1 | THR- 486 | 2.68 | 153.18 | H-Bond (Protein Donor) |
| C2D | CB | VAL- 487 | 3.65 | 0 | Hydrophobic |
| C5' | CB | VAL- 487 | 4.29 | 0 | Hydrophobic |
| O1A | N | VAL- 487 | 2.9 | 168.73 | H-Bond (Protein Donor) |
| N4 | O | VAL- 594 | 3.19 | 125.74 | H-Bond (Ligand Donor) |
| N4 | O | THR- 596 | 2.82 | 156.35 | H-Bond (Ligand Donor) |
| N3 | N | ILE- 598 | 3.11 | 157.62 | H-Bond (Protein Donor) |
| O2 | N | ASN- 599 | 2.81 | 132.18 | H-Bond (Protein Donor) |
| C1' | CB | LEU- 602 | 4.38 | 0 | Hydrophobic |
| C1' | CB | ALA- 603 | 4.26 | 0 | Hydrophobic |
| C4D | CG | GLN- 606 | 3.7 | 0 | Hydrophobic |
| N8' | OE1 | GLN- 606 | 2.76 | 137.92 | H-Bond (Ligand Donor) |
| N4 | O | LYS- 668 | 3.02 | 145.7 | H-Bond (Ligand Donor) |
| O2A | N | ILE- 670 | 2.76 | 147.19 | H-Bond (Protein Donor) |
| O2A | N | GLY- 671 | 2.91 | 144.78 | H-Bond (Protein Donor) |
| C9' | CG | GLU- 672 | 4.47 | 0 | Hydrophobic |
