sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.250 Å
X-ray
2016-02-08
| Name: | Histidine triad nucleotide-binding protein 1 |
|---|---|
| ID: | HINT1_HUMAN |
| AC: | P49773 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 93 % |
| B | 7 % |
| B-Factor: | 11.721 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.524 | 320.625 |
| % Hydrophobic | % Polar |
|---|---|
| 57.89 | 42.11 |
| According to VolSite | |
| HET Code: | BS5 |
|---|---|
| Formula: | C20H29N9O7S2 |
| Molecular weight: | 571.630 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.78 % |
| Polar Surface area: | 269.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 7 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -29.9385 | 5.56258 | -28.3641 |
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 |
| C1' | CZ | PHE- 19 | 4.35 | 0 | Hydrophobic |
| C4' | CZ | PHE- 19 | 4.12 | 0 | Hydrophobic |
| O2' | OD2 | ASP- 43 | 3.5 | 131.45 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 43 | 2.6 | 168.1 | H-Bond (Ligand Donor) |
| N3 | N | ILE- 44 | 3.35 | 157.45 | H-Bond (Protein Donor) |
| C1' | CD1 | LEU- 53 | 3.99 | 0 | Hydrophobic |
| C4' | CD1 | LEU- 53 | 4.26 | 0 | Hydrophobic |
| OP1 | ND2 | ASN- 99 | 2.74 | 155.17 | H-Bond (Protein Donor) |
| CAB | CB | SER- 107 | 3.99 | 0 | Hydrophobic |
| NBB | OG | SER- 107 | 2.55 | 121.11 | H-Bond (Ligand Donor) |
| OP2 | OG | SER- 107 | 3.13 | 139.43 | H-Bond (Protein Donor) |
| C5' | CG2 | VAL- 108 | 4.04 | 0 | Hydrophobic |
| OP2 | N | VAL- 108 | 3.14 | 150.67 | H-Bond (Protein Donor) |
| N5' | NE2 | HIS- 112 | 2.74 | 140.12 | H-Bond (Ligand Donor) |
| OP1 | NE2 | HIS- 114 | 3.1 | 167.47 | H-Bond (Protein Donor) |
| O3' | O | HOH- 343 | 2.76 | 149.39 | H-Bond (Protein Donor) |
