sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2013-05-30
| 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 | 17 % |
| B | 83 % |
| B-Factor: | 26.292 |
|---|---|
| Number of residues: | 56 |
| Including | |
| Standard Amino Acids: | 51 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | CA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.804 | 1667.250 |
| % Hydrophobic | % Polar |
|---|---|
| 37.65 | 62.35 |
| According to VolSite | |
| HET Code: | NAP |
|---|---|
| Formula: | C21H25N7O17P3 |
| Molecular weight: | 740.381 g/mol |
| DrugBank ID: | DB03461 |
| Buried Surface Area: | 60.31 % |
| 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 |
|---|---|---|
| -16.1952 | -44.6944 | -10.4614 |
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 |
| C3N | CB | ALA- 74 | 4.33 | 0 | Hydrophobic |
| O7N | N | THR- 75 | 2.82 | 174.55 | H-Bond (Protein Donor) |
| O7N | OG1 | THR- 75 | 3.21 | 154.42 | H-Bond (Protein Donor) |
| O2D | N | THR- 77 | 3.3 | 158.55 | H-Bond (Protein Donor) |
| O3D | NH2 | ARG- 82 | 3.08 | 167.51 | H-Bond (Protein Donor) |
| O7N | ND2 | ASN- 96 | 2.83 | 145.56 | H-Bond (Protein Donor) |
| C2D | CD1 | LEU- 250 | 4.22 | 0 | Hydrophobic |
| O2X | NZ | LYS- 260 | 2.93 | 159.85 | H-Bond (Protein Donor) |
| O2X | NZ | LYS- 260 | 2.93 | 0 | Ionic (Protein Cationic) |
| C1B | CD1 | LEU- 288 | 4.09 | 0 | Hydrophobic |
| C4D | CB | THR- 311 | 4.31 | 0 | Hydrophobic |
| O4D | N | THR- 311 | 3.17 | 166.79 | H-Bond (Protein Donor) |
| O1A | N | VAL- 312 | 2.95 | 153.52 | H-Bond (Protein Donor) |
| C3B | CG1 | VAL- 312 | 4.05 | 0 | Hydrophobic |
| O2A | N | THR- 313 | 3.05 | 149.17 | H-Bond (Protein Donor) |
| O1X | CZ | ARG- 314 | 3.68 | 0 | Ionic (Protein Cationic) |
| O3X | CZ | ARG- 314 | 3.49 | 0 | Ionic (Protein Cationic) |
| O1X | NE | ARG- 314 | 2.73 | 157.83 | H-Bond (Protein Donor) |
| O3X | NH2 | ARG- 314 | 2.69 | 173.67 | H-Bond (Protein Donor) |
| O3X | NE | ARG- 314 | 3.41 | 131.62 | H-Bond (Protein Donor) |
| O3X | NE2 | HIS- 315 | 2.86 | 176.34 | H-Bond (Protein Donor) |
| N6A | O | ASN- 328 | 3.14 | 164.09 | H-Bond (Ligand Donor) |
| N1A | N | ASN- 328 | 3.15 | 162.31 | H-Bond (Protein Donor) |
| O3D | O | HOH- 668 | 2.55 | 178.36 | H-Bond (Ligand Donor) |
