sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.880 Å
X-ray
2014-05-22
| Name: | Isocitrate dehydrogenase [NADP] cytoplasmic |
|---|---|
| ID: | IDHC_HUMAN |
| AC: | O75874 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.1.1.42 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 95 % |
| B | 5 % |
| B-Factor: | 26.834 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.327 | 1252.125 |
| % Hydrophobic | % Polar |
|---|---|
| 38.81 | 61.19 |
| According to VolSite | |
| HET Code: | NAP |
|---|---|
| Formula: | C21H25N7O17P3 |
| Molecular weight: | 740.381 g/mol |
| DrugBank ID: | DB03461 |
| Buried Surface Area: | 53.31 % |
| Polar Surface area: | 405.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 4 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -3.58544 | 23.7516 | 92.1366 |
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 |
| O7N | N | THR- 75 | 2.9 | 174.47 | H-Bond (Protein Donor) |
| O2D | N | THR- 77 | 3.01 | 157.97 | H-Bond (Protein Donor) |
| O3D | NH2 | ARG- 82 | 3.01 | 153.3 | H-Bond (Protein Donor) |
| N6A | NE2 | HIS- 309 | 3.31 | 144.28 | H-Bond (Ligand Donor) |
| O1A | N | GLY- 310 | 2.86 | 166.01 | H-Bond (Protein Donor) |
| C4D | CB | THR- 311 | 4.04 | 0 | Hydrophobic |
| O4D | N | THR- 311 | 3.07 | 167.75 | H-Bond (Protein Donor) |
| O2A | N | VAL- 312 | 2.76 | 150.84 | H-Bond (Protein Donor) |
| C3B | CG1 | VAL- 312 | 3.94 | 0 | Hydrophobic |
| C5D | CB | THR- 313 | 4.28 | 0 | Hydrophobic |
| O2X | CZ | ARG- 314 | 3.74 | 0 | Ionic (Protein Cationic) |
| O3X | CZ | ARG- 314 | 3.48 | 0 | Ionic (Protein Cationic) |
| O2X | NH2 | ARG- 314 | 2.93 | 175.34 | H-Bond (Protein Donor) |
| O3X | NE | ARG- 314 | 2.57 | 153.96 | H-Bond (Protein Donor) |
| O2X | NE2 | HIS- 315 | 2.78 | 171.37 | H-Bond (Protein Donor) |
| N6A | O | ASN- 328 | 2.88 | 164.63 | H-Bond (Ligand Donor) |
| N1A | N | ASN- 328 | 2.92 | 153.96 | H-Bond (Protein Donor) |
| N7N | O | HOH- 2098 | 2.93 | 158.85 | H-Bond (Ligand Donor) |
