sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2014-01-23
| Name: | GTP-binding nuclear protein Ran |
|---|---|
| ID: | RAN_HUMAN |
| AC: | P62826 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 93 % |
| B | 7 % |
| B-Factor: | 57.489 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.564 | 1029.375 |
| % Hydrophobic | % Polar |
|---|---|
| 39.02 | 60.98 |
| According to VolSite | |
| HET Code: | GTP |
|---|---|
| Formula: | C10H12N5O14P3 |
| Molecular weight: | 519.149 g/mol |
| DrugBank ID: | DB04137 |
| Buried Surface Area: | 81.14 % |
| Polar Surface area: | 335.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -7.52081 | -19.5154 | 26.5281 |
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 |
| O3B | N | GLY- 20 | 2.92 | 168.59 | H-Bond (Protein Donor) |
| O1B | N | GLY- 22 | 2.82 | 140.91 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 23 | 3.25 | 160.53 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 23 | 3.26 | 154.83 | H-Bond (Protein Donor) |
| O1B | N | LYS- 23 | 2.59 | 166.82 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 23 | 3.25 | 0 | Ionic (Protein Cationic) |
| O1B | NZ | LYS- 23 | 3.26 | 0 | Ionic (Protein Cationic) |
| O2B | N | THR- 24 | 3.15 | 163.58 | H-Bond (Protein Donor) |
| O1A | N | THR- 25 | 3.18 | 161.85 | H-Bond (Protein Donor) |
| O1A | OG1 | THR- 25 | 2.93 | 157.41 | H-Bond (Protein Donor) |
| C2' | CZ | PHE- 35 | 4.27 | 0 | Hydrophobic |
| O2' | O | LYS- 37 | 2.68 | 148.76 | H-Bond (Ligand Donor) |
| O3' | O | LYS- 38 | 2.65 | 125.66 | H-Bond (Ligand Donor) |
| O3G | OH | TYR- 39 | 2.65 | 145.8 | H-Bond (Protein Donor) |
| C5' | CD1 | TYR- 39 | 3.9 | 0 | Hydrophobic |
| C4' | CB | TYR- 39 | 4.19 | 0 | Hydrophobic |
| O1G | N | THR- 42 | 2.99 | 158.36 | H-Bond (Protein Donor) |
| N7 | ND2 | ASN- 122 | 3.41 | 129.12 | H-Bond (Protein Donor) |
| N1 | OD1 | ASP- 125 | 3.06 | 167.84 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 125 | 3.2 | 132.61 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 125 | 2.74 | 160.82 | H-Bond (Ligand Donor) |
| O6 | N | LYS- 152 | 3.26 | 122.15 | H-Bond (Protein Donor) |
| O1G | MG | MG- 301 | 2.19 | 0 | Metal Acceptor |
| O2B | MG | MG- 301 | 2.13 | 0 | Metal Acceptor |
