2.600 Å
X-ray
2005-07-01
Name: | Cell death protein 4 |
---|---|
ID: | CED4_CAEEL |
AC: | P30429 |
Organism: | Caenorhabditis elegans |
Reign: | Eukaryota |
TaxID: | 6239 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 75.693 |
---|---|
Number of residues: | 40 |
Including | |
Standard Amino Acids: | 39 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 0 |
Cofactors: | |
Metals: | MG |
Ligandability | Volume (Å3) |
---|---|
0.537 | 1971.000 |
% Hydrophobic | % Polar |
---|---|
50.68 | 49.32 |
According to VolSite |
HET Code: | ATP |
---|---|
Formula: | C10H12N5O13P3 |
Molecular weight: | 503.149 g/mol |
DrugBank ID: | DB00171 |
Buried Surface Area: | 74.05 % |
Polar Surface area: | 319.88 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 17 |
H-Bond Donors: | 3 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 4 |
Cationic atoms: | 0 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 8 |
X | Y | Z |
---|---|---|
96.0145 | 48.6215 | 75.4147 |
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 |
N6 | O | TYR- 131 | 2.91 | 160.61 | H-Bond (Ligand Donor) |
O1G | N | GLY- 162 | 3.28 | 160.37 | H-Bond (Protein Donor) |
O2B | N | GLY- 162 | 3.27 | 137.15 | H-Bond (Protein Donor) |
O3B | N | GLY- 162 | 3.26 | 125.79 | H-Bond (Protein Donor) |
O2B | N | GLY- 164 | 3.19 | 158.78 | H-Bond (Protein Donor) |
O2B | N | LYS- 165 | 3.21 | 163.68 | H-Bond (Protein Donor) |
O1B | N | SER- 166 | 3.1 | 165.46 | H-Bond (Protein Donor) |
O1A | N | VAL- 167 | 3.01 | 161.77 | H-Bond (Protein Donor) |
C5' | CG2 | VAL- 167 | 3.38 | 0 | Hydrophobic |
O3G | NH2 | ARG- 273 | 2.71 | 172.37 | H-Bond (Protein Donor) |
O3G | NE | ARG- 273 | 3.42 | 130.51 | H-Bond (Protein Donor) |
O3G | CZ | ARG- 273 | 3.49 | 0 | Ionic (Protein Cationic) |
C1' | CB | PRO- 330 | 4.13 | 0 | Hydrophobic |
C4' | CB | ALA- 331 | 4.18 | 0 | Hydrophobic |
C1' | CB | MET- 334 | 4.5 | 0 | Hydrophobic |
C2' | CG | PRO- 368 | 4.35 | 0 | Hydrophobic |
O3G | OH | TYR- 369 | 2.62 | 139.91 | H-Bond (Protein Donor) |
C3' | CB | TYR- 369 | 3.5 | 0 | Hydrophobic |
C4' | CD1 | TYR- 369 | 3.53 | 0 | Hydrophobic |
O2G | MG | MG- 550 | 2.3 | 0 | Metal Acceptor |
O1B | MG | MG- 550 | 2.37 | 0 | Metal Acceptor |