sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.550 Å
X-ray
2013-02-18
| Name: | Isocitrate dehydrogenase [NADP], mitochondrial |
|---|---|
| ID: | IDHP_HUMAN |
| AC: | P48735 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.1.1.42 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 44 % |
| B | 56 % |
| B-Factor: | 12.418 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.414 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 69.03 | 30.97 |
| According to VolSite | |
| HET Code: | 1K9 |
|---|---|
| Formula: | C21H18F3N3O3S2 |
| Molecular weight: | 481.511 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 81.73 % |
| Polar Surface area: | 123.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -1.19516 | -14.911 | 28.4003 |
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 |
| CAM | CD2 | LEU- 160 | 4.37 | 0 | Hydrophobic |
| CAL | CD2 | LEU- 160 | 3.94 | 0 | Hydrophobic |
| CAR | CH2 | TRP- 164 | 3.73 | 0 | Hydrophobic |
| CAR | CD1 | ILE- 168 | 4.39 | 0 | Hydrophobic |
| FAD | CG1 | ILE- 290 | 4.01 | 0 | Hydrophobic |
| CAG | CD1 | ILE- 290 | 4.11 | 0 | Hydrophobic |
| CAI | CG1 | VAL- 294 | 4.4 | 0 | Hydrophobic |
| SAV | CB | VAL- 294 | 4.5 | 0 | Hydrophobic |
| CAR | CG1 | VAL- 297 | 4.12 | 0 | Hydrophobic |
| SAV | CG1 | VAL- 297 | 3.69 | 0 | Hydrophobic |
| SAV | CD2 | LEU- 298 | 4.2 | 0 | Hydrophobic |
| CAL | CD2 | LEU- 298 | 3.69 | 0 | Hydrophobic |
| CAQ | CZ3 | TRP- 306 | 4.25 | 0 | Hydrophobic |
| FAE | CE2 | TYR- 311 | 3.45 | 0 | Hydrophobic |
| FAD | CE2 | TYR- 311 | 3.54 | 0 | Hydrophobic |
| FAE | CB | ASP- 312 | 4.2 | 0 | Hydrophobic |
| FAF | CB | ASP- 312 | 3.93 | 0 | Hydrophobic |
| CAG | CB | ASP- 312 | 4.09 | 0 | Hydrophobic |
| FAD | CG2 | VAL- 315 | 3.45 | 0 | Hydrophobic |
| FAE | CB | VAL- 315 | 4.2 | 0 | Hydrophobic |
| FAF | CB | VAL- 315 | 4.25 | 0 | Hydrophobic |
| CAO | CG1 | VAL- 315 | 3.47 | 0 | Hydrophobic |
| CAG | CG1 | VAL- 315 | 3.99 | 0 | Hydrophobic |
| FAF | CG | GLN- 316 | 4.02 | 0 | Hydrophobic |
| CAI | CB | GLN- 316 | 4.15 | 0 | Hydrophobic |
| NAS | OE1 | GLN- 316 | 2.56 | 167.27 | H-Bond (Ligand Donor) |
| NAT | OE1 | GLN- 316 | 2.98 | 139.53 | H-Bond (Ligand Donor) |
| NAU | OE1 | GLN- 316 | 2.86 | 143.48 | H-Bond (Ligand Donor) |
| OAA | NE2 | GLN- 316 | 2.88 | 151.4 | H-Bond (Protein Donor) |
| CAP | CG1 | ILE- 319 | 3.82 | 0 | Hydrophobic |
| CAP | CD1 | ILE- 319 | 4.04 | 0 | Hydrophobic |
| CBA | CD1 | ILE- 319 | 3.59 | 0 | Hydrophobic |
| CBD | CG2 | ILE- 319 | 3.86 | 0 | Hydrophobic |
| CBC | CG2 | ILE- 319 | 3.73 | 0 | Hydrophobic |
| CAM | CG2 | ILE- 319 | 3.69 | 0 | Hydrophobic |
| CAR | CD1 | LEU- 320 | 3.97 | 0 | Hydrophobic |
