2.500 Å
X-ray
2009-09-05
Name: | Lombricine kinase |
---|---|
ID: | Q8T6T7_URECA |
AC: | Q8T6T7 |
Organism: | Urechis caupo |
Reign: | Eukaryota |
TaxID: | 6431 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 30.084 |
---|---|
Number of residues: | 28 |
Including | |
Standard Amino Acids: | 26 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 2 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.312 | 668.250 |
% Hydrophobic | % Polar |
---|---|
38.89 | 61.11 |
According to VolSite |
HET Code: | ADP |
---|---|
Formula: | C10H12N5O10P2 |
Molecular weight: | 424.177 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 62.6 % |
Polar Surface area: | 260.7 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 14 |
H-Bond Donors: | 3 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 3 |
Cationic atoms: | 0 |
Rule of Five Violation: | 1 |
Rotatable Bonds: | 6 |
X | Y | Z |
---|---|---|
15.511 | 19.0907 | 17.5754 |
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 |
N1 | OG | SER- 115 | 2.73 | 156.44 | H-Bond (Protein Donor) |
O2B | NH2 | ARG- 117 | 3.01 | 126.96 | H-Bond (Protein Donor) |
O2B | NH1 | ARG- 117 | 2.72 | 136.53 | H-Bond (Protein Donor) |
O2B | CZ | ARG- 117 | 3.24 | 0 | Ionic (Protein Cationic) |
C1' | CD | ARG- 117 | 4.18 | 0 | Hydrophobic |
O3B | NH1 | ARG- 119 | 3.08 | 130.69 | H-Bond (Protein Donor) |
O3B | NE | ARG- 119 | 2.67 | 152.6 | H-Bond (Protein Donor) |
O3B | CZ | ARG- 119 | 3.28 | 0 | Ionic (Protein Cationic) |
O3' | NE2 | HIS- 178 | 3.18 | 133.44 | H-Bond (Protein Donor) |
O2B | NH1 | ARG- 223 | 3.29 | 157.95 | H-Bond (Protein Donor) |
O3B | NE | ARG- 279 | 2.94 | 128.14 | H-Bond (Protein Donor) |
O3B | CZ | ARG- 279 | 3.94 | 0 | Ionic (Protein Cationic) |
N7 | OG | SER- 281 | 2.7 | 148.41 | H-Bond (Protein Donor) |
N6 | OG | SER- 281 | 3.04 | 143.52 | H-Bond (Ligand Donor) |
DuAr | DuAr | HIS- 283 | 3.49 | 0 | Aromatic Face/Face |
O2A | NH1 | ARG- 307 | 2.96 | 148.11 | H-Bond (Protein Donor) |
O2' | O | THR- 309 | 2.85 | 165.04 | H-Bond (Ligand Donor) |
O2A | N | GLU- 312 | 2.76 | 122.01 | H-Bond (Protein Donor) |
O1B | O | HOH- 426 | 3.48 | 179.98 | H-Bond (Protein Donor) |