sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2009-08-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.100 | 4.100 | 4.100 | 0.000 | 4.100 | 1 |
| Name: | Pantothenate synthetase |
|---|---|
| ID: | PANC_MYCTU |
| AC: | P9WIL5 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 6.3.2.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 21.090 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.721 | 931.500 |
| % Hydrophobic | % Polar |
|---|---|
| 40.58 | 59.42 |
| According to VolSite | |
| HET Code: | A6D |
|---|---|
| Formula: | C17H18N6O5S2 |
| Molecular weight: | 450.492 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.45 % |
| Polar Surface area: | 215.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 1.14103 | -9.9298 | 34.7328 |
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 |
| SAR | CB | PRO- 38 | 4.05 | 0 | Hydrophobic |
| SAS | CG | MET- 40 | 3.91 | 0 | Hydrophobic |
| CAK | CG | MET- 40 | 4.11 | 0 | Hydrophobic |
| CAF | SD | MET- 40 | 3.59 | 0 | Hydrophobic |
| CBA | CD1 | LEU- 50 | 4.09 | 0 | Hydrophobic |
| CBB | CD1 | LEU- 50 | 3.82 | 0 | Hydrophobic |
| CAH | CB | ASN- 69 | 3.82 | 0 | Hydrophobic |
| CAT | CG1 | VAL- 139 | 4.43 | 0 | Hydrophobic |
| CAF | CG2 | VAL- 139 | 3.91 | 0 | Hydrophobic |
| CAH | CG1 | VAL- 142 | 3.99 | 0 | Hydrophobic |
| CAL | CE1 | PHE- 157 | 4.22 | 0 | Hydrophobic |
| OAC | N | GLY- 158 | 2.9 | 167.96 | H-Bond (Protein Donor) |
| N7 | NZ | LYS- 160 | 3.09 | 136.01 | H-Bond (Protein Donor) |
| OAD | OD2 | ASP- 161 | 2.75 | 152.68 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 187 | 3.01 | 174.85 | H-Bond (Protein Donor) |
| N6 | O | VAL- 187 | 3.08 | 168.22 | H-Bond (Ligand Donor) |
| N6 | O | MET- 195 | 2.82 | 164.43 | H-Bond (Ligand Donor) |
| OAC | O | HOH- 312 | 2.7 | 168.58 | H-Bond (Ligand Donor) |
