2.300 Å
X-ray
2005-10-28
Name: | Ribonucleoside-diphosphate reductase large chain 1 |
---|---|
ID: | RIR1_YEAST |
AC: | P21524 |
Organism: | Saccharomyces cerevisiae |
Reign: | Eukaryota |
TaxID: | 559292 |
EC Number: | 1.17.4.1 |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 38.152 |
---|---|
Number of residues: | 34 |
Including | |
Standard Amino Acids: | 32 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 2 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.313 | 526.500 |
% Hydrophobic | % Polar |
---|---|
39.10 | 60.90 |
According to VolSite |
HET Code: | GCQ |
---|---|
Formula: | C9H10F2N3O10P2 |
Molecular weight: | 420.134 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 72.22 % |
Polar Surface area: | 229.55 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 12 |
H-Bond Donors: | 2 |
Rings: | 2 |
Aromatic rings: | 0 |
Anionic atoms: | 3 |
Cationic atoms: | 0 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 6 |
X | Y | Z |
---|---|---|
23.7642 | 53.061 | 16.2359 |
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 |
O3B | OG | SER- 202 | 2.96 | 157.47 | H-Bond (Protein Donor) |
O3B | N | SER- 202 | 2.79 | 173.67 | H-Bond (Protein Donor) |
C4' | CB | SER- 217 | 4.46 | 0 | Hydrophobic |
C1' | CB | SER- 217 | 4.3 | 0 | Hydrophobic |
F1 | SG | CYS- 218 | 3.77 | 0 | Hydrophobic |
O2 | N | GLY- 246 | 2.97 | 126.15 | H-Bond (Protein Donor) |
F2 | CD | ARG- 293 | 3.64 | 0 | Hydrophobic |
F1 | CD2 | LEU- 427 | 3.37 | 0 | Hydrophobic |
C3' | SG | CYS- 428 | 3.43 | 0 | Hydrophobic |
O1A | N | THR- 608 | 2.58 | 147.34 | H-Bond (Protein Donor) |
O2A | N | ALA- 609 | 3.07 | 137.06 | H-Bond (Protein Donor) |
O1B | N | SER- 610 | 3.3 | 131.95 | H-Bond (Protein Donor) |
O1B | N | THR- 611 | 2.67 | 160.95 | H-Bond (Protein Donor) |
O1B | OG1 | THR- 611 | 2.7 | 146.86 | H-Bond (Protein Donor) |