sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2009-04-23
| Name: | 5,10-methenyltetrahydromethanopterin hydrogenase |
|---|---|
| ID: | HMD_METJA |
| AC: | Q58194 |
| Organism: | Methanocaldococcus jannaschii |
| Reign: | Archaea |
| TaxID: | 243232 |
| EC Number: | 1.12.98.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 46.682 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | FE2 |
| Ligandability | Volume (Å3) |
|---|---|
| 1.133 | 735.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.88 | 43.12 |
| According to VolSite | |
| HET Code: | I2C |
|---|---|
| Formula: | C19H22N6O10P |
| Molecular weight: | 525.386 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.51 % |
| Polar Surface area: | 253.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 23.6253 | 9.32783 | 31.6656 |
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 |
| O3' | N | GLY- 9 | 2.99 | 133.58 | H-Bond (Protein Donor) |
| O2P | N | CYS- 10 | 2.82 | 160.19 | H-Bond (Protein Donor) |
| O2 | NE2 | HIS- 14 | 2.97 | 144.73 | H-Bond (Protein Donor) |
| N2A | O | SER- 63 | 3.07 | 133.09 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 64 | 2.8 | 159.03 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 64 | 3.19 | 137.31 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 64 | 2.74 | 148.07 | H-Bond (Ligand Donor) |
| C2' | CB | PRO- 114 | 3.81 | 0 | Hydrophobic |
| C2' | CB | PRO- 115 | 4.33 | 0 | Hydrophobic |
| C3' | SG | CYS- 118 | 4.39 | 0 | Hydrophobic |
| N2A | OD1 | ASP- 135 | 2.8 | 150.4 | H-Bond (Ligand Donor) |
| N1A | OD2 | ASP- 135 | 2.98 | 172.2 | H-Bond (Ligand Donor) |
| C7 | CZ2 | TRP- 148 | 3.88 | 0 | Hydrophobic |
| C5M | CE2 | TRP- 148 | 4.1 | 0 | Hydrophobic |
| C7 | CB | ALA- 175 | 4.02 | 0 | Hydrophobic |
| O8 | N | ALA- 176 | 3.1 | 156 | H-Bond (Protein Donor) |
| C7 | CB | ALA- 176 | 4.32 | 0 | Hydrophobic |
| C7 | CG2 | THR- 177 | 3.88 | 0 | Hydrophobic |
| C5M | CG2 | THR- 177 | 3.53 | 0 | Hydrophobic |
| O8 | FE | FE2- 360 | 2.76 | 0 | Metal Acceptor |
