1.870 Å
X-ray
2012-09-14
Name: | Prothrombin |
---|---|
ID: | THRB_HUMAN |
AC: | P00734 |
Organism: | Homo sapiens |
Reign: | Eukaryota |
TaxID: | 9606 |
EC Number: | 3.4.21.5 |
Chain Name: | Percentage of Residues within binding site |
---|---|
B | 100 % |
B-Factor: | 21.534 |
---|---|
Number of residues: | 34 |
Including | |
Standard Amino Acids: | 32 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 2 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.416 | 367.875 |
% Hydrophobic | % Polar |
---|---|
42.20 | 57.80 |
According to VolSite |
HET Code: | M6S |
---|---|
Formula: | C23H36N6O3 |
Molecular weight: | 444.570 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 66.04 % |
Polar Surface area: | 146.72 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 4 |
H-Bond Donors: | 5 |
Rings: | 3 |
Aromatic rings: | 1 |
Anionic atoms: | 0 |
Cationic atoms: | 2 |
Rule of Five Violation: | 0 |
Rotatable Bonds: | 9 |
X | Y | Z |
---|---|---|
16.0616 | -13.0416 | 22.3192 |
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 |
C26 | CB | HIS- 79 | 4.37 | 0 | Hydrophobic |
C26 | CE2 | TYR- 83 | 3.93 | 0 | Hydrophobic |
C26 | CH2 | TRP- 86 | 3.74 | 0 | Hydrophobic |
C6 | CD2 | LEU- 132 | 4.38 | 0 | Hydrophobic |
C26 | CD2 | LEU- 132 | 3.89 | 0 | Hydrophobic |
C3 | CG1 | ILE- 209 | 3.74 | 0 | Hydrophobic |
C4 | CD1 | ILE- 209 | 3.75 | 0 | Hydrophobic |
C23 | OD2 | ASP- 229 | 3.58 | 0 | Ionic (Ligand Cationic) |
C23 | OD1 | ASP- 229 | 3.63 | 0 | Ionic (Ligand Cationic) |
N24 | OD2 | ASP- 229 | 2.75 | 156.69 | H-Bond (Ligand Donor) |
N25 | OD1 | ASP- 229 | 2.81 | 143.59 | H-Bond (Ligand Donor) |
C19 | CB | ALA- 230 | 4.08 | 0 | Hydrophobic |
N2 | OE1 | GLU- 232 | 3.3 | 146.38 | H-Bond (Ligand Donor) |
C19 | CG1 | VAL- 255 | 3.82 | 0 | Hydrophobic |
N15 | O | SER- 256 | 3.24 | 167.3 | H-Bond (Ligand Donor) |
C1 | CE3 | TRP- 257 | 4.18 | 0 | Hydrophobic |
C3 | CE3 | TRP- 257 | 4.3 | 0 | Hydrophobic |
C5 | CE3 | TRP- 257 | 3.96 | 0 | Hydrophobic |
C6 | CB | TRP- 257 | 4.13 | 0 | Hydrophobic |
N7 | O | GLY- 258 | 2.88 | 158.76 | H-Bond (Ligand Donor) |
O0 | N | GLY- 258 | 3.3 | 164.86 | H-Bond (Protein Donor) |
C3 | CG | GLU- 259 | 4.09 | 0 | Hydrophobic |
N24 | O | GLY- 260 | 2.85 | 140.5 | H-Bond (Ligand Donor) |
O30 | N | GLY- 260 | 2.92 | 165.93 | H-Bond (Protein Donor) |
C21 | SG | CYS- 261 | 4.28 | 0 | Hydrophobic |