sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.980 Å
X-ray
2012-09-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.100 | 5.100 | 5.100 | 0.000 | 5.100 | 2 |
| Name: | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit |
|---|---|
| ID: | OGT1_HUMAN |
| AC: | O15294 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 56.361 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 45 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.821 | 745.875 |
| % Hydrophobic | % Polar |
|---|---|
| 39.82 | 60.18 |
| According to VolSite | |
| HET Code: | 12V |
|---|---|
| Formula: | C17H25N3O16P2S |
| Molecular weight: | 621.403 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.45 % |
| Polar Surface area: | 341.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 7 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -107.395 | 52.6392 | 81.2199 |
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 |
| O7' | NE2 | HIS- 498 | 2.92 | 146.83 | H-Bond (Protein Donor) |
| C8' | CE | MET- 501 | 3.69 | 0 | Hydrophobic |
| S5' | CB | PRO- 559 | 3.95 | 0 | Hydrophobic |
| C6' | CB | PRO- 559 | 4.14 | 0 | Hydrophobic |
| C4B | CG | PRO- 559 | 3.91 | 0 | Hydrophobic |
| C6' | CB | THR- 560 | 4.04 | 0 | Hydrophobic |
| C6' | CD1 | LEU- 563 | 3.57 | 0 | Hydrophobic |
| O4' | O | LEU- 653 | 2.67 | 162.03 | H-Bond (Ligand Donor) |
| C8' | CG | PRO- 656 | 3.96 | 0 | Hydrophobic |
| C4' | CZ | PHE- 694 | 4.31 | 0 | Hydrophobic |
| O2A | NE2 | GLN- 839 | 2.68 | 156.4 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 842 | 2.94 | 167.66 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 842 | 2.94 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 842 | 3.95 | 0 | Ionic (Protein Cationic) |
| N3 | O | ALA- 896 | 2.78 | 153.46 | H-Bond (Ligand Donor) |
| O4 | N | ALA- 896 | 3.08 | 168.11 | H-Bond (Protein Donor) |
| O2' | NZ | LYS- 898 | 2.52 | 135.05 | H-Bond (Protein Donor) |
| C8' | SG | CYS- 917 | 3.53 | 0 | Hydrophobic |
| N2' | ND1 | HIS- 920 | 2.92 | 131.61 | H-Bond (Ligand Donor) |
| O3' | ND1 | HIS- 920 | 3.11 | 147.24 | H-Bond (Ligand Donor) |
| O2B | N | HIS- 920 | 3.04 | 123.91 | H-Bond (Protein Donor) |
| C3' | CB | HIS- 920 | 3.77 | 0 | Hydrophobic |
| O1' | OG1 | THR- 921 | 3.02 | 177.53 | H-Bond (Protein Donor) |
| C3B | CG2 | THR- 921 | 3.78 | 0 | Hydrophobic |
| O2B | N | THR- 922 | 3.32 | 158.39 | H-Bond (Protein Donor) |
| O2' | OD2 | ASP- 925 | 2.72 | 170.49 | H-Bond (Ligand Donor) |
