sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.750 Å
X-ray
2014-08-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.720 | 7.840 | 7.840 | 0.120 | 7.960 | 2 |
| Name: | Macrophage colony-stimulating factor 1 receptor |
|---|---|
| ID: | CSF1R_HUMAN |
| AC: | P07333 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 38.174 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.113 | 421.875 |
| % Hydrophobic | % Polar |
|---|---|
| 56.00 | 44.00 |
| According to VolSite | |
| HET Code: | STI |
|---|---|
| Formula: | C29H32N7O |
| Molecular weight: | 494.611 g/mol |
| DrugBank ID: | DB00619 |
| Buried Surface Area: | 66.1 % |
| Polar Surface area: | 87.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 38.9165 | 13.3537 | 75.6624 |
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 |
| C5 | CD1 | LEU- 588 | 3.9 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 596 | 3.96 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 596 | 4.21 | 0 | Hydrophobic |
| C5 | CB | ALA- 614 | 4.4 | 0 | Hydrophobic |
| C20 | CB | ALA- 614 | 4.18 | 0 | Hydrophobic |
| C17 | CD | LYS- 616 | 4.24 | 0 | Hydrophobic |
| C20 | CB | LYS- 616 | 3.54 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 616 | 3.86 | 157.62 | Pi/Cation |
| N21 | OE2 | GLU- 633 | 2.98 | 138.83 | H-Bond (Ligand Donor) |
| C25 | CG | GLU- 633 | 3.89 | 0 | Hydrophobic |
| C17 | SD | MET- 637 | 3.6 | 0 | Hydrophobic |
| C23 | SD | MET- 637 | 4.4 | 0 | Hydrophobic |
| C25 | CG | MET- 637 | 4.01 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 640 | 4.46 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 647 | 4.14 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 661 | 3.87 | 0 | Hydrophobic |
| N13 | OG1 | THR- 663 | 3.03 | 137.87 | H-Bond (Ligand Donor) |
| C20 | CG2 | THR- 663 | 3.75 | 0 | Hydrophobic |
| C19 | CG2 | THR- 663 | 3.39 | 0 | Hydrophobic |
| N3 | N | CYS- 666 | 2.83 | 168.25 | H-Bond (Protein Donor) |
| N51 | O | ILE- 775 | 3.14 | 146.94 | H-Bond (Ligand Donor) |
| N51 | O | HIS- 776 | 3.31 | 120.9 | H-Bond (Ligand Donor) |
| C5 | CD1 | LEU- 785 | 3.83 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 785 | 4.34 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 785 | 3.96 | 0 | Hydrophobic |
| O29 | N | ASP- 796 | 3.23 | 135.91 | H-Bond (Protein Donor) |
| C23 | CB | ASP- 796 | 3.84 | 0 | Hydrophobic |
| C12 | CZ | PHE- 797 | 3.4 | 0 | Hydrophobic |
