1.650 Å
X-ray
2008-03-17
Name: | Gag-Pol polyprotein |
---|---|
ID: | POL_HV1BR |
AC: | P03367 |
Organism: | Human immunodeficiency virus type 1 group M subtype B |
Reign: | Viruses |
TaxID: | 11686 |
EC Number: | 3.4.23.16 |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 53 % |
B | 47 % |
B-Factor: | 18.419 |
---|---|
Number of residues: | 46 |
Including | |
Standard Amino Acids: | 45 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 1 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
1.181 | 951.750 |
% Hydrophobic | % Polar |
---|---|
45.04 | 54.96 |
According to VolSite |
HET Code: | YDP |
---|---|
Formula: | C28H38N5O6S2 |
Molecular weight: | 604.761 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 65.1 % |
Polar Surface area: | 194.3 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 6 |
H-Bond Donors: | 3 |
Rings: | 3 |
Aromatic rings: | 2 |
Anionic atoms: | 0 |
Cationic atoms: | 1 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 12 |
X | Y | Z |
---|---|---|
5.89037 | 2.27812 | -14.0873 |
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 |
C11 | CD2 | LEU- 23 | 3.56 | 0 | Hydrophobic |
C12 | CD2 | LEU- 23 | 3.68 | 0 | Hydrophobic |
N22 | OD1 | ASP- 25 | 2.83 | 135.65 | H-Bond (Ligand Donor) |
N22 | OD2 | ASP- 25 | 2.94 | 144.22 | H-Bond (Ligand Donor) |
N22 | OD2 | ASP- 25 | 2.75 | 145.93 | H-Bond (Ligand Donor) |
N22 | OD1 | ASP- 25 | 2.83 | 0 | Ionic (Ligand Cationic) |
N22 | OD2 | ASP- 25 | 2.94 | 0 | Ionic (Ligand Cationic) |
N22 | OD1 | ASP- 25 | 2.84 | 0 | Ionic (Ligand Cationic) |
N22 | OD2 | ASP- 25 | 2.75 | 0 | Ionic (Ligand Cationic) |
C18 | CB | ALA- 28 | 3.5 | 0 | Hydrophobic |
C7 | CB | ALA- 28 | 3.53 | 0 | Hydrophobic |
O2 | N | ASP- 30 | 2.57 | 134.33 | H-Bond (Protein Donor) |
O3 | N | ASP- 30 | 2.68 | 152.58 | H-Bond (Protein Donor) |
N2 | OD1 | ASP- 30 | 2.82 | 160.99 | H-Bond (Ligand Donor) |
C18 | CG2 | VAL- 32 | 3.87 | 0 | Hydrophobic |
C5 | CB | ILE- 47 | 3.89 | 0 | Hydrophobic |
C18 | CD1 | ILE- 47 | 4.13 | 0 | Hydrophobic |
C3 | CD1 | ILE- 50 | 4.44 | 0 | Hydrophobic |
C19 | CG1 | ILE- 50 | 4.06 | 0 | Hydrophobic |
C28 | CG2 | ILE- 50 | 4.13 | 0 | Hydrophobic |
O12 | N | ILE- 50 | 2.61 | 165.97 | H-Bond (Protein Donor) |
C13 | CG | PRO- 81 | 4.04 | 0 | Hydrophobic |
C10 | CG1 | VAL- 82 | 4.42 | 0 | Hydrophobic |
C12 | CG1 | VAL- 82 | 4.11 | 0 | Hydrophobic |
C10 | CD1 | ILE- 84 | 4.44 | 0 | Hydrophobic |
C33 | CD1 | ILE- 84 | 3.65 | 0 | Hydrophobic |
C11 | CG1 | ILE- 84 | 4.45 | 0 | Hydrophobic |
C12 | CD1 | ILE- 84 | 4.04 | 0 | Hydrophobic |
C21 | CD1 | ILE- 84 | 4.18 | 0 | Hydrophobic |
C37 | CD1 | ILE- 84 | 3.63 | 0 | Hydrophobic |