1.950 Å
X-ray
2015-01-23
| Name: | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc |
|---|---|
| ID: | P71968_MYCTU |
| AC: | P71968 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.665 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.382 | 367.875 |
| % Hydrophobic | % Polar |
|---|---|
| 45.87 | 54.13 |
| According to VolSite | |

| HET Code: | TMQ |
|---|---|
| Formula: | C19H23N5O3 |
| Molecular weight: | 369.418 g/mol |
| DrugBank ID: | DB01157 |
| Buried Surface Area: | 66.13 % |
| Polar Surface area: | 117.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 17.939 | 26.362 | 21.5083 |
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 |
| N24 | OD1 | ASN- 44 | 2.99 | 142.52 | H-Bond (Ligand Donor) |
| N25 | O | ASN- 44 | 2.68 | 166.55 | H-Bond (Ligand Donor) |
| C4A | CG2 | ILE- 46 | 3.99 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 46 | 3.92 | 0 | Hydrophobic |
| C9 | CB | SER- 59 | 4.2 | 0 | Hydrophobic |
| C5 | CB | SER- 59 | 4.09 | 0 | Hydrophobic |
| C6 | CB | SER- 59 | 3.93 | 0 | Hydrophobic |
| C8 | CB | ALA- 63 | 3.63 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 67 | 3.31 | 130.49 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 67 | 2.54 | 162.9 | H-Bond (Ligand Donor) |
| N24 | OD1 | ASP- 67 | 2.74 | 163.14 | H-Bond (Ligand Donor) |
| C21 | CG | ARG- 68 | 4.12 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 71 | 4.12 | 0 | Hydrophobic |
| C21 | CD1 | PHE- 71 | 3.41 | 0 | Hydrophobic |
| C22 | CE1 | PHE- 71 | 3.45 | 0 | Hydrophobic |
| C4A | CE2 | PHE- 71 | 3.45 | 0 | Hydrophobic |
| C9 | CG | GLU- 91 | 4.13 | 0 | Hydrophobic |
| C16 | CB | GLU- 91 | 4.29 | 0 | Hydrophobic |
| N25 | O | GLU- 193 | 3.16 | 122.49 | H-Bond (Ligand Donor) |
| N24 | OG1 | THR- 214 | 3.28 | 128.05 | H-Bond (Ligand Donor) |
| C17 | C4N | NAP- 301 | 3.73 | 0 | Hydrophobic |
| O20 | O | HOH- 452 | 3.11 | 179.98 | H-Bond (Protein Donor) |