sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.190 Å
X-ray
2009-06-05
| Name: | Kinesin-like protein KIF11 |
|---|---|
| ID: | KIF11_HUMAN |
| AC: | P52732 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 88 % |
| B | 12 % |
| B-Factor: | 16.907 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.282 | 1015.875 |
| % Hydrophobic | % Polar |
|---|---|
| 47.84 | 52.16 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.2 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 5.50926 | 8.73455 | 32.7999 |
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 |
| O1B | N | GLY- 110 | 3.35 | 139.73 | H-Bond (Protein Donor) |
| O1B | N | LYS- 111 | 3.08 | 152.56 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 111 | 2.7 | 171.67 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 111 | 2.7 | 0 | Ionic (Protein Cationic) |
| O2B | N | THR- 112 | 3.24 | 149.87 | H-Bond (Protein Donor) |
| C2' | CD1 | PHE- 113 | 3.76 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 113 | 3.81 | 0 | Aromatic Face/Face |
| O3' | OE2 | GLU- 118 | 3.36 | 152.08 | H-Bond (Ligand Donor) |
| O2' | OE2 | GLU- 118 | 2.86 | 167.13 | H-Bond (Ligand Donor) |
| N3B | OD1 | ASN- 229 | 3.04 | 157.42 | H-Bond (Ligand Donor) |
| O2G | OG | SER- 232 | 2.8 | 171.25 | H-Bond (Protein Donor) |
| O3G | N | SER- 233 | 2.79 | 162.4 | H-Bond (Protein Donor) |
| C1' | CD1 | ILE- 250 | 4.09 | 0 | Hydrophobic |
| O2G | O | HOH- 394 | 2.87 | 163.1 | H-Bond (Protein Donor) |
| N6 | O | HOH- 414 | 3.4 | 160.12 | H-Bond (Ligand Donor) |
| O3G | MG | MG- 501 | 2.25 | 0 | Metal Acceptor |
| O2B | MG | MG- 501 | 2.11 | 0 | Metal Acceptor |
