1.550 Å
X-ray
2011-11-26
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 |
---|---|
H | 100 % |
B-Factor: | 17.959 |
---|---|
Number of residues: | 39 |
Including | |
Standard Amino Acids: | 38 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 1 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.625 | 361.125 |
% Hydrophobic | % Polar |
---|---|
45.79 | 54.21 |
According to VolSite |
HET Code: | 1TS |
---|---|
Formula: | C32H35ClN7O6S |
Molecular weight: | 681.182 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 60.06 % |
Polar Surface area: | 217.68 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 8 |
H-Bond Donors: | 5 |
Rings: | 4 |
Aromatic rings: | 3 |
Anionic atoms: | 0 |
Cationic atoms: | 1 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 13 |
X | Y | Z |
---|---|---|
16.5199 | -14.7813 | 23.2347 |
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 |
C34 | CB | HIS- 57 | 4.45 | 0 | Hydrophobic |
C12 | CH2 | TRP- 60 | 4.34 | 0 | Hydrophobic |
C34 | CZ3 | TRP- 60 | 4.3 | 0 | Hydrophobic |
C1 | CH2 | TRP- 60 | 3.6 | 0 | Hydrophobic |
C10 | CE1 | TYR- 60 | 4.29 | 0 | Hydrophobic |
C1 | CZ | TYR- 60 | 3.52 | 0 | Hydrophobic |
CL | CB | ASN- 98 | 4.37 | 0 | Hydrophobic |
C10 | CD1 | LEU- 99 | 3.68 | 0 | Hydrophobic |
C5 | CD2 | LEU- 99 | 4.16 | 0 | Hydrophobic |
C34 | CD2 | LEU- 99 | 3.8 | 0 | Hydrophobic |
CL | CG2 | ILE- 174 | 4.05 | 0 | Hydrophobic |
C3 | CD1 | ILE- 174 | 4.3 | 0 | Hydrophobic |
C27 | OD2 | ASP- 189 | 3.71 | 0 | Ionic (Ligand Cationic) |
C27 | OD1 | ASP- 189 | 3.8 | 0 | Ionic (Ligand Cationic) |
N29 | OD1 | ASP- 189 | 3.03 | 148.09 | H-Bond (Ligand Donor) |
N28 | OD2 | ASP- 189 | 2.95 | 160.63 | H-Bond (Ligand Donor) |
C25 | CB | ALA- 190 | 4.24 | 0 | Hydrophobic |
C26 | CG1 | VAL- 213 | 3.81 | 0 | Hydrophobic |
N19 | O | SER- 214 | 3.01 | 170.25 | H-Bond (Ligand Donor) |
CL | CD2 | TRP- 215 | 3.41 | 0 | Hydrophobic |
C3 | CB | TRP- 215 | 4.46 | 0 | Hydrophobic |
N11 | O | GLY- 216 | 3.11 | 123.04 | H-Bond (Ligand Donor) |
O14 | N | GLY- 216 | 3.23 | 166.55 | H-Bond (Protein Donor) |
C8 | CB | GLU- 217 | 3.58 | 0 | Hydrophobic |
N28 | O | GLY- 219 | 2.8 | 129.08 | H-Bond (Ligand Donor) |
C23 | SG | CYS- 220 | 4.47 | 0 | Hydrophobic |