sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2008-07-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.680 | 9.680 | 9.680 | 0.000 | 9.680 | 1 |
| Name: | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase |
|---|---|
| ID: | MTNN_VIBCH |
| AC: | Q9KPI8 |
| Organism: | Vibrio cholerae serotype O1 |
| Reign: | Bacteria |
| TaxID: | 243277 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 14 % |
| C | 86 % |
| B-Factor: | 41.147 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.199 | 293.625 |
| % Hydrophobic | % Polar |
|---|---|
| 75.86 | 24.14 |
| According to VolSite | |
| HET Code: | BIG |
|---|---|
| Formula: | C16H26N5OS |
| Molecular weight: | 336.476 g/mol |
| DrugBank ID: | DB07463 |
| Buried Surface Area: | 79.44 % |
| Polar Surface area: | 117.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 22.3863 | -9.80091 | 13.4083 |
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' | SD | MET- 9 | 4.05 | 0 | Hydrophobic |
| C23 | CE | MET- 9 | 4.42 | 0 | Hydrophobic |
| C3' | CG2 | ILE- 50 | 3.82 | 0 | Hydrophobic |
| S5' | CG2 | ILE- 50 | 4.39 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 50 | 3.87 | 0 | Hydrophobic |
| S5' | CG1 | VAL- 102 | 4.39 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 102 | 4.19 | 0 | Hydrophobic |
| C21 | CD2 | PHE- 105 | 3.97 | 0 | Hydrophobic |
| C23 | CD1 | PHE- 105 | 4.19 | 0 | Hydrophobic |
| C20 | CE2 | PHE- 105 | 3.95 | 0 | Hydrophobic |
| C21 | CB | ALA- 113 | 3.86 | 0 | Hydrophobic |
| C5 | CE2 | PHE- 152 | 3.41 | 0 | Hydrophobic |
| C5' | CD2 | PHE- 152 | 3.41 | 0 | Hydrophobic |
| N6 | O | VAL- 153 | 3.05 | 156.85 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 153 | 3.05 | 175.49 | H-Bond (Protein Donor) |
| C5' | SD | MET- 174 | 3.51 | 0 | Hydrophobic |
| O3' | OE2 | GLU- 175 | 2.78 | 172.37 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 175 | 3.49 | 130.5 | H-Bond (Ligand Donor) |
| N7 | OD1 | ASP- 198 | 3.39 | 145.28 | H-Bond (Ligand Donor) |
| N7 | OD2 | ASP- 198 | 2.76 | 155.41 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASP- 198 | 2.96 | 166.72 | H-Bond (Ligand Donor) |
| C20 | CE1 | PHE- 208 | 4.08 | 0 | Hydrophobic |
| C23 | CE1 | PHE- 208 | 4.31 | 0 | Hydrophobic |
| C4' | CZ | PHE- 208 | 4.06 | 0 | Hydrophobic |
| N1' | O | HOH- 302 | 2.98 | 162.53 | H-Bond (Ligand Donor) |
