sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2001-09-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.000 | 9.000 | 9.000 | 0.000 | 9.000 | 1 |
| Name: | S-methyl-5'-thioadenosine phosphorylase |
|---|---|
| ID: | MTAP_HUMAN |
| AC: | Q13126 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 13.876 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.169 | 401.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.10 | 47.90 |
| According to VolSite | |
| HET Code: | MTM |
|---|---|
| Formula: | C12H22N5O2S |
| Molecular weight: | 300.400 g/mol |
| DrugBank ID: | DB02158 |
| Buried Surface Area: | 76.18 % |
| Polar Surface area: | 151.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 7 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 3 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 60.4585 | 17.0712 | 28.8453 |
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 |
| CS | CG2 | THR- 18 | 4.26 | 0 | Hydrophobic |
| C3' | CG | PRO- 69 | 4 | 0 | Hydrophobic |
| S5' | CZ | PHE- 177 | 3.74 | 0 | Hydrophobic |
| C5' | CE1 | PHE- 177 | 4.15 | 0 | Hydrophobic |
| C2' | CB | ASN- 195 | 4.32 | 0 | Hydrophobic |
| C2' | CG | MET- 196 | 3.79 | 0 | Hydrophobic |
| C3' | SD | MET- 196 | 3.73 | 0 | Hydrophobic |
| O2' | N | MET- 196 | 2.79 | 152.22 | H-Bond (Protein Donor) |
| N7 | OD2 | ASP- 220 | 2.79 | 173.25 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASP- 220 | 2.86 | 153.69 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASP- 222 | 3.06 | 168.24 | H-Bond (Ligand Donor) |
| CS | CG2 | VAL- 233 | 4.29 | 0 | Hydrophobic |
| S5' | CG1 | VAL- 236 | 3.78 | 0 | Hydrophobic |
| N1 | O | HOH- 510 | 2.85 | 179.97 | H-Bond (Protein Donor) |
