sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2013-08-28
| Name: | Rap guanine nucleotide exchange factor 4 |
|---|---|
| ID: | RPGF4_MOUSE |
| AC: | Q9EQZ6 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| E | 100 % |
| B-Factor: | 43.927 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.968 | 563.625 |
| % Hydrophobic | % Polar |
|---|---|
| 51.50 | 48.50 |
| According to VolSite | |
| HET Code: | CMP |
|---|---|
| Formula: | C10H11N5O6P |
| Molecular weight: | 328.198 g/mol |
| DrugBank ID: | DB02527 |
| Buried Surface Area: | 75.34 % |
| Polar Surface area: | 167.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 4.73964 | -18.1072 | -60.0494 |
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' | CE1 | PHE- 367 | 3.84 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 386 | 4.16 | 0 | Hydrophobic |
| C4' | CB | PHE- 403 | 4.42 | 0 | Hydrophobic |
| C1' | CB | PHE- 403 | 4.29 | 0 | Hydrophobic |
| O2' | N | GLY- 404 | 3.32 | 160.06 | H-Bond (Protein Donor) |
| O2P | N | ALA- 407 | 3.02 | 155.73 | H-Bond (Protein Donor) |
| O2P | NH1 | ARG- 414 | 2.95 | 137.52 | H-Bond (Protein Donor) |
| O1P | N | ALA- 415 | 3.45 | 162.9 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 416 | 3.97 | 0 | Hydrophobic |
| C4' | CD1 | ILE- 418 | 4.31 | 0 | Hydrophobic |
| C2' | CD2 | LEU- 449 | 3.87 | 0 | Hydrophobic |
| N7 | N | LYS- 450 | 3.36 | 158.26 | H-Bond (Protein Donor) |
| N6 | O | LYS- 450 | 3.09 | 157.62 | H-Bond (Ligand Donor) |
| N1 | NZ | LYS- 489 | 2.94 | 174.84 | H-Bond (Protein Donor) |
