1.990 Å
X-ray
2015-03-17
Name: | Xanthine dehydrogenase/oxidase |
---|---|
ID: | XDH_RAT |
AC: | P22985 |
Organism: | Rattus norvegicus |
Reign: | Eukaryota |
TaxID: | 10116 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 17.228 |
---|---|
Number of residues: | 61 |
Including | |
Standard Amino Acids: | 56 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 4 |
Cofactors: | NAI |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.840 | 583.875 |
% Hydrophobic | % Polar |
---|---|
45.66 | 54.34 |
According to VolSite |
HET Code: | FAD |
---|---|
Formula: | C27H31N9O15P2 |
Molecular weight: | 783.534 g/mol |
DrugBank ID: | DB03147 |
Buried Surface Area: | 78.47 % |
Polar Surface area: | 381.7 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 22 |
H-Bond Donors: | 7 |
Rings: | 6 |
Aromatic rings: | 3 |
Anionic atoms: | 2 |
Cationic atoms: | 0 |
Rule of Five Violation: | 3 |
Rotatable Bonds: | 13 |
X | Y | Z |
---|---|---|
-4.98692 | 22.8363 | -90.7115 |
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 |
C8M | CD1 | LEU- 74 | 4.24 | 0 | Hydrophobic |
C3B | CD | LYS- 255 | 4.45 | 0 | Hydrophobic |
C2B | CB | LEU- 256 | 4.18 | 0 | Hydrophobic |
O2B | O | LEU- 256 | 2.83 | 135.61 | H-Bond (Ligand Donor) |
O2A | N | VAL- 258 | 2.72 | 164.99 | H-Bond (Protein Donor) |
O1P | N | GLY- 259 | 2.86 | 153.9 | H-Bond (Protein Donor) |
O2A | N | ASN- 260 | 2.96 | 155.8 | H-Bond (Protein Donor) |
C8M | CB | THR- 261 | 4.16 | 0 | Hydrophobic |
C2' | CB | THR- 261 | 4.41 | 0 | Hydrophobic |
O2' | OG1 | THR- 261 | 2.97 | 153.87 | H-Bond (Ligand Donor) |
O2P | N | THR- 261 | 2.97 | 156.56 | H-Bond (Protein Donor) |
O2P | OG1 | THR- 261 | 2.55 | 171.39 | H-Bond (Protein Donor) |
O1A | N | GLU- 262 | 2.98 | 148.46 | H-Bond (Protein Donor) |
C5B | CB | GLU- 262 | 3.75 | 0 | Hydrophobic |
C5' | CG | GLU- 262 | 3.71 | 0 | Hydrophobic |
C2' | CG | GLU- 262 | 4.08 | 0 | Hydrophobic |
O3' | OE2 | GLU- 262 | 2.78 | 164.38 | H-Bond (Ligand Donor) |
O1A | N | ILE- 263 | 2.96 | 173.07 | H-Bond (Protein Donor) |
C5B | CG1 | ILE- 263 | 4.38 | 0 | Hydrophobic |
C3B | CD1 | ILE- 263 | 3.76 | 0 | Hydrophobic |
C3' | CZ | PHE- 336 | 3.93 | 0 | Hydrophobic |
C6 | CB | ALA- 337 | 3.44 | 0 | Hydrophobic |
C8M | CG2 | VAL- 341 | 4.26 | 0 | Hydrophobic |
C7M | CG2 | VAL- 341 | 3.62 | 0 | Hydrophobic |
C8 | CG1 | VAL- 341 | 4.2 | 0 | Hydrophobic |
C4' | CB | ALA- 345 | 3.62 | 0 | Hydrophobic |
O4' | O | SER- 346 | 2.82 | 134.09 | H-Bond (Ligand Donor) |
O5' | N | SER- 346 | 3.29 | 136.48 | H-Bond (Protein Donor) |
O1P | N | SER- 346 | 3.01 | 155.43 | H-Bond (Protein Donor) |
O1P | OG | SER- 346 | 2.81 | 165.08 | H-Bond (Protein Donor) |
O2 | ND2 | ASN- 350 | 2.77 | 147.26 | H-Bond (Protein Donor) |
O3' | ND2 | ASN- 350 | 3.08 | 154.23 | H-Bond (Protein Donor) |
C3' | CB | ASN- 350 | 4.11 | 0 | Hydrophobic |
C1B | CG2 | ILE- 352 | 3.94 | 0 | Hydrophobic |
O2 | N | ASP- 359 | 3 | 163.77 | H-Bond (Protein Donor) |
N3 | OD1 | ASP- 359 | 2.82 | 141.55 | H-Bond (Ligand Donor) |
N6A | O | LEU- 403 | 3.04 | 149.5 | H-Bond (Ligand Donor) |
N1A | N | LEU- 403 | 2.93 | 151.17 | H-Bond (Protein Donor) |
C6 | C4N | NAI- 3005 | 3.86 | 0 | Hydrophobic |
C9A | C4N | NAI- 3005 | 4.13 | 0 | Hydrophobic |
C1' | C2D | NAI- 3005 | 3.72 | 0 | Hydrophobic |
N5 | O | HOH- 3117 | 2.87 | 148.66 | H-Bond (Protein Donor) |