sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2008-03-29
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.570 | 6.570 | 6.570 | 0.000 | 6.570 | 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 |
|---|---|
| A | 100 % |
| B-Factor: | 17.619 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.592 | 1123.875 |
| % Hydrophobic | % Polar |
|---|---|
| 38.44 | 61.56 |
| According to VolSite | |
| HET Code: | 52H |
|---|---|
| Formula: | C16H23N6O8S |
| Molecular weight: | 459.454 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.87 % |
| Polar Surface area: | 222.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 14.606 | 9.80045 | 1.61697 |
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 |
| CAB | CB | PRO- 38 | 3.87 | 0 | Hydrophobic |
| CAC | CB | PRO- 38 | 4.45 | 0 | Hydrophobic |
| C5' | CB | THR- 39 | 4.17 | 0 | Hydrophobic |
| OAG | N | MET- 40 | 2.88 | 168.42 | H-Bond (Protein Donor) |
| CAX | CG | MET- 40 | 3.88 | 0 | Hydrophobic |
| O4' | ND1 | HIS- 47 | 3.27 | 123.23 | H-Bond (Protein Donor) |
| C1' | CD2 | LEU- 50 | 3.85 | 0 | Hydrophobic |
| C4' | CD2 | LEU- 50 | 3.59 | 0 | Hydrophobic |
| OAH | NE2 | GLN- 72 | 2.93 | 166.65 | H-Bond (Protein Donor) |
| CAA | CG1 | VAL- 139 | 4.43 | 0 | Hydrophobic |
| CAA | CG1 | VAL- 142 | 3.62 | 0 | Hydrophobic |
| CAA | CG2 | VAL- 143 | 4.13 | 0 | Hydrophobic |
| CAC | CG2 | VAL- 143 | 4.16 | 0 | Hydrophobic |
| CAC | CE2 | PHE- 157 | 3.62 | 0 | Hydrophobic |
| O3' | N | GLY- 158 | 2.93 | 163.6 | H-Bond (Protein Donor) |
| O2' | N | GLY- 158 | 3.31 | 123.06 | H-Bond (Protein Donor) |
| O2' | OD2 | ASP- 161 | 2.68 | 155.76 | H-Bond (Ligand Donor) |
| OAH | OE1 | GLN- 164 | 2.77 | 138.69 | H-Bond (Ligand Donor) |
| OAE | NE2 | GLN- 164 | 3.07 | 162 | H-Bond (Protein Donor) |
| N1 | N | VAL- 187 | 2.9 | 177.32 | H-Bond (Protein Donor) |
| N6 | O | VAL- 187 | 3.1 | 166.42 | H-Bond (Ligand Donor) |
| N6 | O | MET- 195 | 2.9 | 157.13 | H-Bond (Ligand Donor) |
| O2' | O | HOH- 718 | 3.31 | 179.97 | H-Bond (Protein Donor) |
| O3' | O | HOH- 723 | 2.66 | 160.69 | H-Bond (Ligand Donor) |
